|
AMRFinderPlus |
amrfinderplus |
tabular, fasta |
"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. |
2023-05-12 |
https://github.com/ncbi/amr |
3.12.8 |
ncbi-amrfinderplus |
4.2.7 |
To update |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Microbiology, Public health and epidemiology, Infectious disease |
Microbiology, Public health and epidemiology, Infectious disease |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus |
amrfinderplus |
AMRFinderPlus |
AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms |
|
1 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
953 |
953 |
45130 |
45130 |
689 |
689 |
17362 |
17362 |
0 |
0 |
0 |
0 |
28 |
28 |
1863 |
1863 |
64355 |
64355 |
1670 |
1670 |
https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=368d1ac0150ea0b6, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=46b6812817c57a01, https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=f8fab0cd6fc30d92, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=9, https://workflowhub.eu/workflows/2024?version=2 |
|
True |
False |
|
ISEScan |
isescan |
txt, tabular, gff, fasta |
"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements." |
2022-09-01 |
https://github.com/xiezhq/ISEScan |
1.7.3 |
isescan |
1.7.3 |
Up-to-date |
Sequence Analysis |
Structural variation detection |
Structural variation detection |
Genomics, DNA structural variation, Sequence analysis, Genetic variation |
Genomics, Sequence analysis, Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan |
ISEScan |
ISEScan |
Automated identification of insertion sequence elements in prokaryotic genomes. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
392 |
392 |
67516 |
67516 |
237 |
237 |
1535 |
1535 |
116 |
116 |
7464 |
7464 |
37 |
37 |
1759 |
1759 |
78274 |
78274 |
782 |
782 |
https://usegalaxy.eu/published/workflow?id=1306ed083d91a852, https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=67ca17ab34b10772, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=13, https://workflowhub.eu/workflows/1513?version=1 |
genome-annotation/bacterial-genome-annotation |
True |
False |
|
abacas |
abacas |
tabular, fasta |
Order and Orientate Contigs |
2019-11-20 |
https://github.com/phac-nml/abacas |
1.1 |
mummer |
3.23 |
To update |
Assembly |
|
|
|
|
nml |
https://github.com/phac-nml/abacas |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
3 |
3 |
3 |
3 |
2 |
2 |
|
|
True |
False |
|
abricate |
abricate, abricate_list, abricate_summary |
tabular, txt |
Mass screening of contigs for antiobiotic resistance genes |
2016-07-29 |
https://github.com/tseemann/abricate |
1.0.1 |
abricate |
1.2.0 |
To update |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Genomics, Microbiology |
Genomics, Microbiology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate |
ABRicate |
ABRicate |
Mass screening of contigs for antimicrobial resistance or virulence genes. |
|
3 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
0 |
4522 |
4679 |
799841 |
821957 |
3401 |
3468 |
401550 |
405363 |
1867 |
2216 |
578174 |
600408 |
85 |
85 |
19178 |
19178 |
1846906 |
1798743 |
10448 |
9875 |
https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=368d1ac0150ea0b6, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=46b6812817c57a01, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=77e5bbd317750915, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f, https://usegalaxy.org.au/published/workflow?id=e20172eb0f30d6cd, https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=9ba6da7dae465d3e, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=cce88bc57b180d09, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=f8fab0cd6fc30d92, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=9, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1495?version=1, https://workflowhub.eu/workflows/2024?version=2, https://workflowhub.eu/workflows/470?version=1 |
microbiome/pathogen-detection-from-nanopore-foodborne-data |
True |
False |
|
abritamr |
abritamr |
tabular, txt |
A pipeline for running AMRfinderPlus and collating results into functional classes |
2023-04-03 |
https://zenodo.org/record/7370628 |
1.0.20 |
abritamr |
1.0.20 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Microbiology, Public health and epidemiology, Infectious disease, Antimicrobial resistance |
Microbiology, Public health and epidemiology, Infectious disease |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr |
abritamr |
abriTAMR |
an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
319 |
319 |
2633 |
2633 |
0 |
0 |
0 |
0 |
97 |
97 |
880 |
880 |
3 |
3 |
5 |
5 |
3518 |
3518 |
419 |
419 |
https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://workflowhub.eu/workflows/634?version=1 |
|
True |
False |
|
abyss |
abyss-pe |
fasta, tabular |
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |
2015-04-14 |
https://github.com/bcgsc/abyss |
2.3.10 |
abyss |
2.3.10 |
Up-to-date |
Assembly |
Genome assembly, De-novo assembly, Scaffolding |
Genome assembly, De-novo assembly, Scaffolding |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss |
abyss |
ABySS |
De novo genome sequence assembler using short reads. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1258 |
1368 |
7148 |
7779 |
183 |
414 |
505 |
1305 |
398 |
398 |
2608 |
2608 |
11 |
11 |
16 |
16 |
11708 |
10277 |
2191 |
1850 |
|
|
True |
False |
|
aldex2 |
aldex2 |
tabular, png, pdf |
Performs analysis Of differential abundance taking sample variation into account |
2022-06-29 |
https://github.com/ggloor/ALDEx_bioc |
1.26.0 |
bioconductor-aldex2 |
1.38.0 |
To update |
Metagenomics |
Statistical inference |
Statistical inference |
Gene expression, Statistics and probability |
Gene expression, Statistics and probability |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 |
aldex2 |
ALDEx2 |
A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
64 |
64 |
356 |
356 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
356 |
356 |
64 |
64 |
|
|
True |
False |
|
amas |
amas_concat, amas_remove, amas_replicate, amas_split, amas_summary |
txt |
AMAS high-throughput alignment manipulation and summaries for phylogenomics |
2025-12-02 |
https://github.com/marekborowiec/AMAS |
1.0 |
amas |
1.0 |
Up-to-date |
Phylogenetics, Sequence Analysis, Statistics |
Nucleic acid sequence analysis, Protein sequence analysis |
Nucleic acid sequence analysis, Protein sequence analysis |
Phylogenomics, Phylogenetics, Sequence analysis, Statistics and probability |
Phylogenomics, Phylogenetics, Statistics and probability |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas |
amas |
AMAS |
AMAS (Alignment Manipulation And Summary), a tool that works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
amplican |
amplican |
csv, tabular, html, txt, rdata, fasta |
AmpliCan is an analysis tool for genome editing. |
2021-09-22 |
https://github.com/valenlab/amplican |
1.14.0 |
bioconductor-amplican |
1.28.0 |
To update |
Sequence Analysis |
Alignment, Standardisation and normalisation |
Alignment, Standardisation and normalisation |
PCR experiment, Statistics and probability |
PCR experiment, Statistics and probability |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican |
amplican |
amplican |
It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
18 |
18 |
85 |
85 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
85 |
85 |
18 |
18 |
|
|
True |
False |
|
ampligone |
ampligone |
fastqsanger, bed |
AmpliGone is a tool which accurately finds and removes primer sequences from NGS reads in an amplicon experiment. |
2025-07-29 |
https://rivm-bioinformatics.github.io/AmpliGone/latest/ |
2.0.1 |
AmpliGone |
2.0.2 |
To update |
Sequence Analysis, Fastq Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
ancombc |
ancombc |
|
Performs analysis of compositions of microbiomes with bias correction. |
2022-07-16 |
https://github.com/FrederickHuangLin/ANCOMBC |
1.4.0 |
bioconductor-ancombc |
2.12.0 |
To update |
Metagenomics |
DNA barcoding |
DNA barcoding |
Microbial ecology, Metagenomics, Taxonomy |
Microbial ecology, Metagenomics, Taxonomy |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc |
ancombc |
ANCOMBC |
Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
20 |
20 |
64 |
64 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
64 |
64 |
20 |
20 |
|
|
True |
False |
|
antismash |
antismash |
html, txt |
Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters |
2015-02-28 |
https://antismash.secondarymetabolites.org |
6.1.1 |
antismash |
8.0.4 |
To update |
Sequence Analysis |
Sequence clustering, Gene prediction, Differential gene expression analysis |
Sequence clustering, Gene prediction, Differential gene expression analysis |
Molecular interactions, pathways and networks, Gene and protein families |
Molecular interactions, pathways and networks, Gene and protein families |
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash |
https://github.com/bgruening/galaxytools/tree/master/tools/antismash |
antismash |
antiSMASH |
Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1083 |
1236 |
29269 |
32703 |
1017 |
1017 |
12499 |
12499 |
280 |
280 |
10622 |
10622 |
6 |
6 |
170 |
170 |
55994 |
52560 |
2539 |
2386 |
https://usegalaxy.eu/published/workflow?id=0461bbd1f96292e2, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=edbaf66c1e97ebdb, https://usegalaxy.eu/published/workflow?id=f141db5179ea8422, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://workflowhub.eu/workflows/1558?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 |
genome-annotation/secondary-metabolite-discovery |
True |
False |
|
argnorm |
argnorm |
tsv |
argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database |
2024-08-28 |
https://github.com/BigDataBiology/argNorm |
1.0.0 |
argnorm |
1.1.0 |
To update |
Genome annotation |
Gene functional annotation |
Gene functional annotation |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm |
argnorm |
argNorm |
argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. |
|
1 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
48 |
48 |
211 |
211 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
91 |
91 |
302 |
302 |
51 |
51 |
https://workflowhub.eu/workflows/2024?version=2, https://workflowhub.eu/workflows/2068?version=1 |
|
True |
False |
|
artic |
artic_guppyplex, artic_minion |
bam, tabular, vcf_bgzip, fasta, txt |
The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building |
2020-04-17 |
https://github.com/artic-network/fieldbioinformatics |
1.7.3 |
artic |
1.8.5 |
To update |
Sequence Analysis |
Sequence alignment |
Sequence alignment |
Genomics |
Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic |
artic |
ARTIC |
A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore |
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
2 |
1 |
0 |
206 |
206 |
13444 |
13459 |
0 |
0 |
0 |
0 |
34 |
34 |
1812 |
1812 |
0 |
0 |
0 |
0 |
15271 |
15256 |
240 |
240 |
https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3, https://workflowhub.eu/workflows/521?version=1 |
|
True |
False |
|
assembly_stats |
assembly_stats |
html |
Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. |
2023-06-21 |
https://github.com/rjchallis/assembly-stats |
17.02 |
rjchallis-assembly-stats |
17.02 |
Up-to-date |
Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
32 |
32 |
32 |
32 |
18 |
18 |
|
|
True |
True |
|
assemblystats |
assemblystats |
tabular, fasta, png |
Summarise an assembly (e.g. N50 metrics) |
2017-10-13 |
https://github.com/phac-nml/galaxy_tools |
1.1.0 |
perl-bioperl |
1.7.8 |
To update |
Assembly |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
autobigs |
autobigs-cli |
csv |
Automated MLST typing from PubMLST and InstitutPasteur. |
2025-02-24 |
https://github.com/Syph-and-VPD-Lab/autoBIGS.cli |
0.6.2 |
autobigs-cli |
0.6.5 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/autobigs |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/autobigs |
AutoBIGS.CLI |
AutoBIGS.CLI |
A command-line interface (CLI) based program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV. Capable of querying a variety of MLST databases from both Institut Pasteur and PubMLST. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
31 |
53 |
53 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
53 |
53 |
31 |
31 |
|
|
True |
False |
|
bakta |
bakta |
tabular, gff3, fasta, txt, json, svg |
"Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." |
2022-09-01 |
https://github.com/oschwengers/bakta |
1.9.4 |
bakta |
1.12.0 |
To update |
Sequence Analysis |
Genome annotation |
Genome annotation |
Genomics, Sequence analysis, Bioinformatics |
Genomics, Sequence analysis, Bioinformatics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta |
bakta |
Bakta |
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1503 |
1503 |
67465 |
67465 |
1017 |
1017 |
14351 |
14351 |
399 |
399 |
33530 |
33530 |
84 |
84 |
3664 |
3664 |
119010 |
119010 |
3003 |
3003 |
https://usegalaxy.eu/published/workflow?id=1306ed083d91a852, https://usegalaxy.eu/published/workflow?id=29c565eff0080e42, https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=67ca17ab34b10772, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=13, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/1488?version=2, https://workflowhub.eu/workflows/1513?version=1 |
genome-annotation/amr-gene-detection, genome-annotation/bacterial-genome-annotation, microbiome/mags-building |
True |
False |
|
bamtools |
bamtools |
txt |
Operate on and transform BAM datasets in various ways using bamtools |
2017-06-09 |
https://github.com/pezmaster31/bamtools |
2.5.2 |
bamtools |
2.5.3 |
To update |
Sequence Analysis, SAM |
Data handling, Sequence alignment analysis |
Data handling, Sequence alignment analysis |
Sequencing, Data management, Sequence analysis |
Sequencing, Sequence analysis |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools |
bamtools |
BamTools |
BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
583 |
746 |
13272 |
15936 |
1177 |
5735 |
56981 |
102230 |
6 |
6 |
283 |
283 |
14 |
14 |
56 |
56 |
118505 |
70592 |
6501 |
1780 |
https://usegalaxy.eu/published/workflow?id=36a4646959829018, https://usegalaxy.eu/published/workflow?id=99022559adf01c4a, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1631?version=1 |
assembly/metagenomics-assembly, microbiome/metagenomics-assembly |
True |
False |
|
bandage |
bandage_image, bandage_info |
jpg, tabular |
Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily |
2018-09-06 |
https://github.com/rrwick/Bandage |
2022.09 |
bandage_ng |
2026.2.1 |
To update |
Visualization |
Sequence assembly visualisation |
Sequence assembly visualisation |
Genomics, Sequence assembly |
Genomics, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage |
bandage |
Bandage |
GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
2 |
2 |
2 |
0 |
5065 |
5359 |
74766 |
78507 |
4846 |
5038 |
63998 |
65491 |
3140 |
3234 |
25266 |
26126 |
317 |
319 |
9763 |
9780 |
179904 |
173793 |
13950 |
13368 |
https://usegalaxy.eu/published/workflow?id=002a51bdef00e14d, https://usegalaxy.eu/published/workflow?id=01fe4c590e608103, https://usegalaxy.eu/published/workflow?id=03be9d62e8e4a129, https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=085c3a4c89d137b5, https://usegalaxy.eu/published/workflow?id=089e5e83b1de0511, https://usegalaxy.eu/published/workflow?id=0ebfab0e957b7267, https://usegalaxy.eu/published/workflow?id=1151052f4393852a, https://usegalaxy.eu/published/workflow?id=1483534f49b826bf, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=17b0a6d3379a4392, https://usegalaxy.eu/published/workflow?id=194a05d42687b524, https://usegalaxy.eu/published/workflow?id=1ac0a15758277730, https://usegalaxy.eu/published/workflow?id=1bb084f1bc102734, https://usegalaxy.eu/published/workflow?id=1cba6eb4aff8dc61, https://usegalaxy.eu/published/workflow?id=1da7ac8eaf891f39, 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assembly/ERGA-post-assembly-QC, assembly/assembly-with-preprocessing, assembly/chloroplast-assembly, assembly/debruijn-graph-assembly, assembly/largegenome, assembly/metagenomics-assembly, assembly/mrsa-illumina, assembly/mrsa-nanopore, microbiome/metagenomics-assembly, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore |
True |
False |
|
bayescan |
BayeScan |
txt |
Detecting natural selection from population-based genetic data |
2017-03-09 |
http://cmpg.unibe.ch/software/BayeScan/index.html |
2.1 |
bayescan |
2.0.1 |
To update |
Sequence Analysis |
Statistical inference |
Statistical inference |
Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism |
Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan |
bayescan |
BayeScan |
BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
28 |
35 |
109 |
136 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
136 |
109 |
35 |
28 |
|
|
True |
False |
|
bbtools |
bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole |
fastqsanger, tabular, fasta, txt, bam, fastq, vcf |
BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. |
2021-10-04 |
https://jgi.doe.gov/data-and-tools/bbtools/ |
39.08 |
bbmap |
39.52 |
To update |
Sequence Analysis |
RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment |
RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment |
Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq |
RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools |
bbmap |
BBMap |
BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. |
|
6 |
3 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
413 |
413 |
25287 |
25287 |
562 |
562 |
10487 |
10487 |
172 |
172 |
3537 |
3537 |
5 |
5 |
134 |
134 |
39445 |
39445 |
1152 |
1152 |
https://usegalaxy.eu/published/workflow?id=d967194ca51ff11e, https://usegalaxy.org.au/published/workflow?id=25f65a29ce3c3ee0, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/519?version=1 |
|
True |
False |
|
bigscape |
bigscape |
html, txt |
Construct sequence similarity networks of BGCs and groups them into GCF |
2024-02-18 |
https://github.com/medema-group/BiG-SCAPE |
1.1.9 |
bigscape |
2.0.2 |
To update |
Metagenomics |
Clustering, Global alignment, Fold recognition |
Clustering, Global alignment, Fold recognition |
Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families |
Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape |
BiG-SCAPE |
BiG-SCAPE |
A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
95 |
95 |
2449 |
2449 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2449 |
2449 |
95 |
95 |
|
|
True |
False |
|
binette |
binette |
tabular |
Binning refinement tool |
2025-01-14 |
https://github.com/genotoul-bioinfo/Binette |
1.2.1 |
binette |
1.2.1 |
Up-to-date |
Metagenomics |
Read binning |
Read binning |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette |
binette |
Binette |
Binette is a fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
11 |
11 |
359 |
359 |
8 |
8 |
17 |
17 |
0 |
0 |
0 |
0 |
1 |
1 |
49 |
49 |
425 |
425 |
20 |
20 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1 |
microbiome/metagenomics-binning |
True |
False |
|
binning_refiner |
bin_refiner |
tabular |
Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. |
2022-02-18 |
https://github.com/songweizhi/Binning_refiner |
1.4.3 |
binning_refiner |
1.4.3 |
Up-to-date |
Metagenomics |
Read binning, Sequence clustering |
Read binning, Sequence clustering |
Metagenomics, Sequence assembly, Microbial ecology |
Metagenomics, Sequence assembly, Microbial ecology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner |
binning_refiner |
Binning_refiner |
Improving genome bins through the combination of different binning programs |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
64 |
64 |
236 |
236 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
236 |
236 |
64 |
64 |
|
|
True |
False |
|
bio_hansel |
bio_hansel |
tabular |
Heidelberg and Enteritidis SNP Elucidation |
2017-09-29 |
https://github.com/phac-nml/bio_hansel |
2.6.1 |
bio_hansel |
2.6.1 |
Up-to-date |
Sequence Analysis |
Genotyping, SNP detection, Genome assembly |
Genotyping, SNP detection, Genome assembly |
Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science |
Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel |
Biohansel |
BioHansel |
BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. |
|
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
36 |
39 |
312 |
397 |
57 |
63 |
538 |
592 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
989 |
850 |
102 |
93 |
|
|
True |
False |
|
biohansel |
biohansel |
tabular, json |
Heidelberg and Enteritidis SNP Elucidation |
2018-08-01 |
https://github.com/phac-nml/biohansel |
2.4.0 |
bio_hansel |
2.6.1 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/biohansel |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
biomformat |
biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table |
biom1, txt |
The biom-format package provides a command line interface and Python API for working with BIOM files. |
2016-06-07 |
https://github.com/biocore/biom-format |
2.1.15 |
biom-format |
2.1.7 |
To update |
Metagenomics |
Formatting |
Formatting |
Laboratory information management, Sequence analysis |
Laboratory information management, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format |
biomformat |
biomformat |
This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. |
|
2 |
2 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
342 |
356 |
16688 |
16852 |
374 |
593 |
2736 |
5533 |
166 |
235 |
2283 |
2833 |
0 |
0 |
0 |
0 |
25218 |
21707 |
1184 |
882 |
https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.eu/published/workflow?id=fb806b88850f3427, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=20d472fc5563a640, https://usegalaxy.org.au/published/workflow?id=4f837b7f90d5ebac, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://usegalaxy.org.au/published/workflow?id=ca6f29110df8dadc, https://usegalaxy.org/published/workflow?id=45f959d5bf505b15, https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/142?version=1, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1 |
microbiome/mgnify-amplicon |
True |
False |
|
biotradis |
bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites |
txt, tabular.gz, bam, csv, pdf |
Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. |
2020-01-17 |
https://www.sanger.ac.uk/science/tools/bio-tradis |
1.4.5 |
biotradis |
1.4.5 |
Up-to-date |
Genome annotation |
Sequence analysis |
Sequence analysis |
Mobile genetic elements, Workflows |
Mobile genetic elements, Workflows |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis |
biotradis |
biotradis |
The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. |
|
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
165 |
176 |
6369 |
6769 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6769 |
6369 |
176 |
165 |
|
|
True |
False |
|
blast2go |
blast2go |
tabular |
Maps BLAST results to GO annotation terms |
2013-09-23 |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go |
0.0.11 |
b2g4pipe |
|
To update |
Ontology Manipulation, Sequence Analysis |
Gene functional annotation |
Gene functional annotation |
Nucleic acid sites, features and motifs |
Nucleic acid sites, features and motifs |
peterjc |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go |
Blast2GO |
Blast2GO |
Bioinformatics platform for high-quality functional annotation and analysis of genomic datasets. It allows analyzing and visualizing newly sequenced genomes by combining state-of-the-art methodologies, standard resources and algorithms. It allows to gain biological insights fast and easy even for completely novel genomes. Perform out-of-the-box the entire workflow of functional annotation of your transcriptomic datasets including its analysis and biological interpretation. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
205 |
303 |
851 |
1255 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
10 |
1265 |
851 |
304 |
205 |
https://usegalaxy.eu/published/workflow?id=33312e5643279e8a |
|
True |
False |
|
blast_rbh |
blast_reciprocal_best_hits |
tabular |
BLAST Reciprocal Best Hits (RBH) from two FASTA files |
2014-05-15 |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh |
0.3.0 |
biopython |
1.70 |
To update |
Fasta Manipulation, Sequence Analysis |
Gene functional annotation, Nucleic acid sequence analysis |
Gene functional annotation, Nucleic acid sequence analysis |
Nucleic acid sites, features and motifs |
Nucleic acid sites, features and motifs |
peterjc |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh |
blast_rbh |
blast_rbh |
This tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
413 |
502 |
25833 |
37031 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
37031 |
25833 |
502 |
413 |
https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a |
|
True |
False |
|
blastxml_to_top_descr |
blastxml_to_top_descr |
tabular |
Make table of top BLAST match descriptions |
2013-09-23 |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr |
0.1.2 |
python |
|
To update |
Convert Formats, Sequence Analysis, Text Manipulation |
Sequence alignment, Sequence annotation |
Sequence alignment, Sequence annotation |
Sequence analysis |
Sequence analysis |
peterjc |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr |
blastxml_to_top_descr |
blastxml_to_top_descr |
This tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
530 |
653 |
263613 |
265902 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
265902 |
263613 |
653 |
530 |
https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4 |
|
True |
False |
|
bmtagger |
bmtagger |
|
remove contaminant reads |
2025-11-12 |
https://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ |
3.101 |
bmtagger |
3.101 |
Up-to-date |
Metagenomics |
Data filtering, Read pre-processing |
Read pre-processing |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger |
bmtagger |
bmtagger |
Best Match Tagger for removing contaminant reads from metagenomics datasets |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
bracken |
est_abundance |
tabular, txt |
Bayesian Reestimation of Abundance with KrakEN |
2019-10-15 |
https://github.com/jenniferlu717/Bracken/releases |
3.1 |
bracken |
3.1 |
Up-to-date |
Sequence Analysis, Metagenomics |
Statistical calculation |
Statistical calculation |
Metagenomics, Microbial ecology |
Metagenomics, Microbial ecology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken |
bracken |
Bracken |
Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample). |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1714 |
1714 |
108307 |
108307 |
804 |
804 |
27569 |
27569 |
265 |
265 |
8873 |
8873 |
59 |
59 |
12432 |
12432 |
157181 |
157181 |
2842 |
2842 |
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ecology/bacterial-isolate-species-contamination-checking, microbiome/taxonomic-profiling, sequence-analysis/quality-contamination-control |
True |
False |
|
busco |
busco |
txt, tabular, png, gff3, fasta |
BUSCO assess genome and annotation completeness |
2017-01-12 |
https://gitlab.com/ezlab/busco/-/releases |
5.8.0 |
busco |
6.0.0 |
To update |
Sequence Analysis, Genome annotation |
Sequence assembly validation |
Sequence assembly validation |
Sequence assembly, Genomics, Transcriptomics, Sequence analysis |
Sequence assembly, Transcriptomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco |
busco |
BUSCO |
Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
5636 |
5838 |
134029 |
137202 |
5194 |
5212 |
58403 |
58497 |
3096 |
3288 |
49227 |
52147 |
262 |
262 |
8860 |
8866 |
256712 |
250519 |
14600 |
14188 |
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https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/1549?version=1, https://workflowhub.eu/workflows/1580?version=1, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/1621?version=1, https://workflowhub.eu/workflows/1641?version=1, https://workflowhub.eu/workflows/1646?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/1746?version=1, https://workflowhub.eu/workflows/2011?version=1, https://workflowhub.eu/workflows/2029?version=1, https://workflowhub.eu/workflows/229?version=1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/605?version=1, https://workflowhub.eu/workflows/606?version=2, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/612?version=25, https://workflowhub.eu/workflows/642?version=25, https://workflowhub.eu/workflows/701?version=1, https://workflowhub.eu/workflows/702?version=1, https://workflowhub.eu/workflows/754?version=1, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1, https://workflowhub.eu/workflows/794?version=2, https://workflowhub.eu/workflows/879?version=1, https://workflowhub.eu/workflows/881?version=5 |
assembly/ERGA-post-assembly-QC, assembly/assembly-quality-control, assembly/hifi-assembly, assembly/hybrid_denovo_assembly, assembly/largegenome, assembly/vgp_genome_assembly, ecology/phylogeny-data-prep, genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short, genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation, genome-annotation/funannotate, genome-annotation/helixer |
True |
False |
|
cami_amber |
biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert |
tabular, html |
Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments |
2024-05-20 |
https://github.com/CAMI-challenge/AMBER |
2.0.7 |
cami-amber |
2.0.7 |
Up-to-date |
Metagenomics |
Read binning |
Read binning |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber |
cami-amber |
AMBER |
AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. The provided metrics were used in the first community benchmarking challenge of the initiative for the Critical Assessment of Metagenomic Interpretation. |
|
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
10522 |
10522 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10522 |
10522 |
8 |
8 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1 |
|
True |
False |
|
canu |
canu |
txt, fasta, fasta.gz |
Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). |
2018-06-07 |
https://github.com/marbl/canu |
2.3 |
canu |
2.3 |
Up-to-date |
Assembly |
De-novo assembly |
De-novo assembly |
Genomics |
Genomics |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/canu |
https://github.com/bgruening/galaxytools/tree/master/tools/canu |
canu |
CANU |
De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
1644 |
1843 |
13768 |
17494 |
0 |
0 |
0 |
0 |
454 |
485 |
3744 |
4325 |
37 |
37 |
480 |
480 |
22299 |
17992 |
2365 |
2135 |
|
|
True |
False |
|
cawlign |
cawlign |
fasta |
Codon-aware alignment of sequences to a reference. |
2025-09-30 |
https://github.com/veg/cawlign |
0.1.15 |
cawlign |
0.1.16 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cawlign |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
cd_hit |
cd_hit |
txt, fasta |
Cluster or compare biological sequence datasets |
2018-02-26 |
http://weizhongli-lab.org/cd-hit/ |
4.8.1 |
cd-hit |
4.8.1 |
Up-to-date |
Sequence Analysis, Fasta Manipulation |
Sequence clustering |
Sequence clustering |
Sequencing |
Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit |
cd-hit |
cd-hit |
Cluster a nucleotide dataset into representative sequences. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
899 |
899 |
20148 |
20148 |
1 |
1 |
2 |
2 |
1 |
1 |
2 |
2 |
57 |
57 |
1174 |
1174 |
21326 |
21326 |
958 |
958 |
https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5 |
|
True |
False |
|
cd_hit_dup |
cd_hit_dup |
fastqsanger, tabular |
simple tool for removing duplicates from sequencing reads |
2015-04-28 |
|
0.0.1 |
cd-hit-auxtools |
4.8.1 |
To update |
Metagenomics, Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup |
|
|
|
|
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
501 |
770 |
7542 |
9437 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9437 |
7542 |
770 |
501 |
https://usegalaxy.org/published/workflow?id=35c2626849348f2c |
|
True |
False |
|
cemitool |
cemitool |
tabular, txt, html |
Gene co-expression network analysis tool |
2022-10-10 |
https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html |
1.30.0 |
bioconductor-cemitool |
1.30.0 |
Up-to-date |
Transcriptomics, RNA, Statistics, Single Cell |
Enrichment analysis, Pathway or network analysis |
Enrichment analysis, Pathway or network analysis |
Gene expression, Transcriptomics, Microarray experiment |
Transcriptomics, Microarray experiment |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool |
cemitool |
CEMiTool |
It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. |
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
45 |
45 |
354 |
354 |
87 |
87 |
584 |
584 |
6 |
6 |
154 |
154 |
0 |
0 |
0 |
0 |
1092 |
1092 |
138 |
138 |
|
|
True |
False |
|
checkm |
checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa |
tabular, zip, fasta, phyloxml, json, newick |
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes |
2022-07-29 |
https://github.com/Ecogenomics/CheckM |
1.2.4 |
checkm-genome |
1.2.4 |
Up-to-date |
Metagenomics |
Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation |
Sequence assembly validation, Sequence composition calculation, Statistical calculation |
Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management |
Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm |
checkm |
CheckM |
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. |
|
10 |
10 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
0 |
0 |
717 |
717 |
12189 |
12189 |
179 |
179 |
1510 |
1510 |
96 |
96 |
2254 |
2254 |
50 |
50 |
1469 |
1469 |
17422 |
17422 |
1042 |
1042 |
https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb, https://workflowhub.eu/workflows/1352?version=4 |
microbiome/mags-building, microbiome/metagenomics-binning |
True |
False |
|
checkm2 |
checkm2 |
tabular |
Rapid assessment of genome bin quality using machine learning |
2024-11-08 |
https://github.com/chklovski/CheckM2 |
1.1.0 |
checkm2 |
1.1.0 |
Up-to-date |
Metagenomics |
Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation |
Sequence assembly validation, Sequence composition calculation, Statistical calculation |
Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management |
Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2 |
checkm |
CheckM |
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
228 |
228 |
1602 |
1602 |
187 |
187 |
1322 |
1322 |
0 |
0 |
0 |
0 |
15 |
15 |
1268 |
1268 |
4192 |
4192 |
430 |
430 |
https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=368d1ac0150ea0b6, https://usegalaxy.eu/published/workflow?id=7371b6918e895e0c, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ba1fda2318046543, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://usegalaxy.eu/published/workflow?id=e532d98f4b368666, https://usegalaxy.fr/published/workflow?id=f0776f7a890b523a, https://usegalaxy.org.au/published/workflow?id=f05ed1e5c5dfffa9, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=a8aee61c2cbaf6ea, https://usegalaxy.org/published/workflow?id=b76a9ce44ea019f1, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/1882?version=3 |
genome-annotation/bacterial-genome-quality-control |
True |
False |
|
checkv |
checkv_end_to_end |
tabular, fasta |
Assess quality of single-contig viral genomes |
2024-09-13 |
https://bitbucket.org/berkeleylab/checkv/ |
1.0.3 |
checkv |
1.0.3 |
Up-to-date |
Metagenomics |
Sequence assembly, Validation, Read mapping |
Sequence assembly, Validation, Read mapping |
Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping |
Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv |
checkv |
CheckV |
CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. |
|
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
83 |
83 |
4527 |
4527 |
1 |
1 |
21 |
21 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4548 |
4548 |
84 |
84 |
https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 |
|
True |
False |
|
chopper |
chopper |
|
Filtering and trimming of fastq files with long read sequencing such as PacBio or ONT. |
2025-07-22 |
https://github.com/wdecoster/chopper |
0.12.0 |
chopper |
0.12.0 |
Up-to-date |
Sequence Analysis, Fastq Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
6 |
6 |
https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=ece3ffe0800e6880 |
|
True |
False |
|
cialign |
cialign |
fasta, txt, png, tsv |
Tool to clean, visualise and analyse a multiple sequence alignment |
2025-08-04 |
https://github.com/KatyBrown/CIAlign |
1.1.4 |
cialign |
1.1.4 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
3 |
3 |
|
|
True |
False |
|
clair3 |
clair3 |
vcf_bgzip |
Symphonizing pileup and full-alignment for high-performance long-read variant calling |
2022-06-15 |
https://github.com/HKU-BAL/Clair3 |
1.0.10 |
clair3 |
1.2.0 |
To update |
Sequence Analysis, Variant Analysis |
Variant calling |
Variant calling |
Molecular genetics |
Molecular genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 |
clair3 |
Clair3 |
Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
328 |
328 |
5269 |
5269 |
52 |
52 |
1858 |
1858 |
13 |
13 |
246 |
246 |
2 |
2 |
54 |
54 |
7427 |
7427 |
395 |
395 |
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microbiome/pathogen-detection-from-nanopore-foodborne-data |
True |
False |
|
clinod |
clinod |
tabular |
NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins |
2013-05-02 |
http://www.compbio.dundee.ac.uk/www-nod/ |
0.1.0 |
clinod |
1.3 |
To update |
Sequence Analysis |
Nucleic acid sequence analysis |
Nucleic acid sequence analysis |
Sequence analysis |
Sequence analysis |
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod |
https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod |
clinod |
clinod |
The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. |
|
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
31 |
585 |
585 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
585 |
585 |
31 |
31 |
|
|
True |
False |
|
clustalw |
clustalw |
clustal, nhx |
ClustalW multiple sequence alignment program for DNA or proteins |
2022-10-02 |
http://www.clustal.org/clustal2/ |
2.1 |
clustalw |
2.1 |
Up-to-date |
Phylogenetics, Sequence Analysis |
Multiple sequence alignment |
Multiple sequence alignment |
Phylogeny, Sequence analysis |
Phylogeny, Sequence analysis |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw |
clustal2 |
Clustal 2 (Clustal W, Clustal X) |
Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
2268 |
2506 |
114395 |
117339 |
3966 |
8263 |
54653 |
99642 |
837 |
966 |
11073 |
13924 |
42 |
43 |
726 |
730 |
231635 |
180847 |
11778 |
7113 |
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ecology/phylogeny-data-prep, genome-annotation/hpc-for-lsgc, microbiome/pathogen-detection-from-nanopore-foodborne-data |
True |
False |
|
codeml |
codeml |
txt |
Detects positive selection |
2017-07-19 |
http://abacus.gene.ucl.ac.uk/software/paml.html |
4.9 |
paml |
4.10.10 |
To update |
Phylogenetics |
Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis |
Probabilistic sequence generation |
Phylogenetics, Sequence analysis |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml |
paml |
PAML |
Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
72 |
84 |
62891 |
63000 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
63000 |
62891 |
84 |
72 |
|
|
True |
False |
|
cojac |
cooc_mutbamscan, cooc_pubmut, cooc_tabmut |
yaml, json, tabular, tsv, csv, html |
co-occurrence of mutations on amplicons |
2022-08-11 |
https://github.com/cbg-ethz/cojac |
0.9.3 |
cojac |
0.9.3 |
Up-to-date |
Metagenomics, Sequence Analysis |
|
|
Genetic variation |
Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac |
cojac |
COJAC |
CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. |
|
2 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
13 |
13 |
2763 |
2763 |
7 |
7 |
20 |
20 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2783 |
2783 |
20 |
20 |
https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b |
|
True |
False |
|
combine_metaphlan2_humann2 |
combine_metaphlan_humann |
tabular |
Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances |
2023-07-20 |
|
0.3.0 |
python |
|
To update |
Metagenomics |
Aggregation |
Aggregation |
Metagenomics, Molecular interactions, pathways and networks |
Metagenomics, Molecular interactions, pathways and networks |
bebatut |
https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 |
https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann |
combine_metaphlan_and_humann |
Combine Metaphlan and HUMAnN |
This tool combine MetaPhlAn outputs and HUMANnN outputs |
|
1 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
112 |
112 |
1972 |
1972 |
31 |
31 |
128 |
128 |
0 |
0 |
0 |
0 |
12 |
12 |
25 |
25 |
2125 |
2125 |
155 |
155 |
https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1466?version=2 |
microbiome/metatranscriptomics |
True |
False |
|
comebin |
comebin |
|
Binning of metagenomic contigs using COntrastive Multi-viEw representation learning |
2025-07-03 |
https://github.com/ziyewang/COMEBin |
1.0.4 |
comebin |
1.0.4 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1 |
|
|
True |
False |
|
comebin_bam |
comebin_bam |
bam |
Generate bam file for COMEBin |
2025-11-07 |
https://github.com/ziyewang/COMEBin |
1.0.4 |
comebin |
1.0.4 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin_bam/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin_bam |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
compare_humann2_output |
compare_humann2_output |
tabular, txt |
Compare outputs of HUMAnN2 for several samples and extract similar and specific information |
2022-10-19 |
|
0.2.0 |
|
|
To update |
Metagenomics |
Comparison |
Comparison |
Metagenomics, Gene and protein families |
Metagenomics, Gene and protein families |
bebatut |
https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output |
https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output |
compare_humann2_outputs |
Compare HUMAnN2 outputs |
This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
23 |
32 |
248 |
332 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
332 |
248 |
32 |
23 |
|
|
True |
False |
|
compleasm |
compleasm |
tsv, gff3, fasta, txt |
Compleasm: a faster and more accurate reimplementation of BUSCO |
2023-12-04 |
https://github.com/huangnengCSU/compleasm |
0.2.6 |
compleasm |
0.2.7 |
To update |
Sequence Analysis |
Sequence assembly validation |
Sequence assembly validation |
Sequence assembly, Genomics, Transcriptomics, Sequence analysis |
Sequence assembly, Transcriptomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm |
compleasm |
Compleasm |
Compleasm: a faster and more accurate reimplementation of BUSCO.It provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
99 |
99 |
675 |
675 |
92 |
92 |
638 |
638 |
20 |
20 |
269 |
269 |
18 |
18 |
449 |
449 |
2031 |
2031 |
229 |
229 |
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|
True |
False |
|
concoct |
concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering |
csv, txt, tabular, fasta, bed |
CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. |
2022-02-18 |
https://github.com/BinPro/CONCOCT |
1.1.0 |
concoct |
1.1.0 |
Up-to-date |
Metagenomics |
Sequence clustering, Read binning |
Sequence clustering, Read binning |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct |
concoct |
CONCOCT |
A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. |
|
5 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
0 |
0 |
107 |
107 |
9955 |
9955 |
19 |
19 |
187 |
187 |
0 |
0 |
0 |
0 |
4 |
4 |
3085 |
3085 |
13227 |
13227 |
130 |
130 |
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microbiome/metagenomics-binning |
True |
False |
|
contig_annotation_tool |
cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise |
tabular, txt |
Contig Annotation Tool (CAT) |
2019-11-27 |
https://github.com/dutilh/CAT |
5.2.3 |
cat |
6.0.1 |
To update |
Metagenomics |
Taxonomic classification, Sequence assembly, Coding region prediction |
Taxonomic classification, Sequence assembly, Coding region prediction |
Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly |
Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat |
cat_bins |
CAT and BAT |
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. |
|
5 |
2 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
0 |
257 |
267 |
17418 |
17676 |
216 |
231 |
1590 |
1750 |
84 |
85 |
848 |
875 |
0 |
0 |
0 |
0 |
20301 |
19856 |
583 |
557 |
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|
True |
False |
|
coverm |
coverm_contig, coverm_genome |
tabular |
CoverM genome and contig wrappers |
2022-04-26 |
https://github.com/wwood/CoverM |
0.7.0 |
coverm |
0.7.0 |
Up-to-date |
Sequence Analysis |
Local alignment |
Local alignment |
Metagenomics, Sequence analysis |
Metagenomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm |
coverm |
CoverM |
Read coverage calculator for metagenomics |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
2 |
0 |
0 |
147 |
147 |
3594 |
3594 |
14 |
14 |
414 |
414 |
11 |
11 |
125 |
125 |
7 |
7 |
565 |
565 |
4698 |
4698 |
179 |
179 |
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assembly/metagenomics-assembly, microbiome/metagenomics-assembly |
True |
False |
|
cryptogenotyper |
CryptoGenotyper |
fasta, tabular, txt |
CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA (18S) and gp60 markers. |
2020-10-14 |
https://github.com/phac-nml/CryptoGenotyper |
1.5.0 |
cryptogenotyper |
1.5.0 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/CryptoGenotyper |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
31 |
31 |
12430 |
12430 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12430 |
12430 |
31 |
31 |
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|
True |
False |
|
cutadapt |
cutadapt |
fastqsanger, txt, json |
Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). |
2018-02-20 |
https://cutadapt.readthedocs.org/en/stable/ |
5.2 |
cutadapt |
5.2 |
Up-to-date |
Fasta Manipulation, Fastq Manipulation, Sequence Analysis |
Sequence trimming, Primer removal, Read pre-processing |
Sequence trimming, Primer removal, Read pre-processing |
Genomics, Probes and primers, Sequencing |
Genomics, Probes and primers, Sequencing |
lparsons |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt |
cutadapt |
Cutadapt |
Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
14131 |
16253 |
330892 |
364942 |
22476 |
26008 |
409500 |
482165 |
4256 |
4631 |
79748 |
86014 |
1579 |
1582 |
59464 |
59550 |
992671 |
879604 |
48474 |
42442 |
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assembly/metagenomics-assembly, assembly/vgp_genome_assembly, contributing/create-new-tutorial, ecology/ENA_Biodiv_submission, epigenetics/atac-seq, genome-annotation/crispr-screen, genome-annotation/tnseq, microbiome/metagenomics-assembly, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, sequence-analysis/quality-control, transcriptomics/clipseq, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-interactome, transcriptomics/rna-seq-reads-to-counts |
True |
False |
|
dada2 |
dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_primerCheck, dada2_removeBimeraDenovo, dada2_seqCounts |
tabular, dada2_dada, dada2_errorrates, pdf, dada2_sequencetable, dada2_mergepairs, dada2_uniques |
DADA2 wrappers |
2019-07-05 |
https://benjjneb.github.io/dada2/index.html |
1.34.0 |
bioconductor-dada2 |
1.38.0 |
To update |
Metagenomics |
Variant calling, DNA barcoding |
Variant calling, DNA barcoding |
Sequencing, Genetic variation, Microbial ecology, Metagenomics |
Sequencing, Genetic variation, Microbial ecology, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 |
dada2 |
dada2 |
This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. |
|
10 |
10 |
11 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
10 |
0 |
865 |
885 |
205808 |
209081 |
1301 |
1344 |
254475 |
270135 |
179 |
179 |
52639 |
52639 |
72 |
72 |
38131 |
38131 |
569986 |
551053 |
2480 |
2417 |
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microbiome/dada-16S |
True |
False |
|
das_tool |
Fasta_to_Contig2Bin, das_tool |
tabular, txt, fasta |
DAS Tool for genome resolved metagenomics |
2022-06-23 |
https://github.com/cmks/DAS_Tool |
1.1.7 |
das_tool |
1.1.7 |
Up-to-date |
Metagenomics |
Read binning |
Read binning |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool |
dastool |
dastool |
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
2 |
0 |
0 |
77 |
77 |
6906 |
6906 |
12 |
12 |
283 |
283 |
0 |
0 |
0 |
0 |
3 |
3 |
1185 |
1185 |
8374 |
8374 |
92 |
92 |
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microbiome/metagenomics-binning |
True |
False |
|
decontam |
decontam |
png, tabular, phyloseq |
Removes decontamination features (ASVs/OTUs) using control samples |
2024-09-13 |
https://github.com/benjjneb/decontam |
1.22.0 |
bioconductor-decontam |
1.30.0 |
To update |
Metagenomics |
Classification |
Classification |
Metagenomics, Microbial ecology, Sequencing |
Metagenomics, Microbial ecology, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam |
decontam |
decontam |
Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
32 |
32 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
32 |
32 |
8 |
8 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 |
|
True |
False |
|
deeparg |
deeparg_predict, deeparg_short_reads |
tabular |
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes |
2024-10-07 |
https://github.com/gaarangoa/deeparg |
1.0.4 |
deeparg |
1.0.4 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction, Antimicrobial resistance prediction |
Antimicrobial resistance prediction, Antimicrobial resistance prediction |
Microbiology |
Microbiology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/deeparg |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/deeparg |
deeparg |
DeepARG |
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. |
|
1 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
20 |
20 |
108 |
108 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
65 |
65 |
173 |
173 |
24 |
24 |
https://workflowhub.eu/workflows/2068?version=1 |
|
True |
False |
|
deseq2 |
deseq2 |
tabular, pdf |
Differential gene expression analysis based on the negative binomial distribution |
2014-12-03 |
https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html |
2.11.40.8 |
bioconductor-deseq2 |
1.50.2 |
To update |
Transcriptomics, RNA, Statistics, Single Cell |
Differential gene expression analysis, RNA-Seq analysis |
Differential gene expression analysis, RNA-Seq analysis |
RNA-Seq |
RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 |
DESeq2 |
DESeq2 |
R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
13707 |
15994 |
110682 |
133936 |
27214 |
37996 |
191581 |
286575 |
2980 |
3614 |
19899 |
24448 |
820 |
824 |
4511 |
4530 |
449489 |
326673 |
58428 |
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transcriptomics/de-novo, transcriptomics/mirna-target-finder, transcriptomics/network-analysis-with-heinz, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/srna |
True |
False |
|
dfast |
dfast |
tabular, fasta, embl, genbank, gff3, txt |
Prokaryotic genome annotation |
2025-04-16 |
https://github.com/nigyta/dfast_core/ |
1.3.6 |
dfast |
1.3.8 |
To update |
Genome annotation |
Genome annotation |
Genome annotation |
Nucleic acid structure analysis, Genomics, Sequence analysis |
Nucleic acid structure analysis, Genomics, Sequence analysis |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/dfast/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/dfast |
dfast |
DFAST |
Flexible prokaryotic genome annotation pipeline for faster genome publication. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
diamond |
bg_diamond, bg_diamond_makedb, bg_diamond_view |
txt, dmnd |
DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. |
2021-03-21 |
https://github.com/bbuchfink/diamond |
2.1.16 |
diamond |
2.1.22 |
To update |
Sequence Analysis |
Sequence alignment analysis |
Sequence alignment analysis |
Sequence analysis, Proteins |
Sequence analysis, Proteins |
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond |
diamond |
Diamond |
Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. |
|
3 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
0 |
1620 |
1706 |
112648 |
114376 |
665 |
1048 |
35921 |
43599 |
446 |
448 |
65850 |
66062 |
125 |
125 |
2180 |
2208 |
226245 |
216599 |
3327 |
2856 |
https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=559f079f6510aa24, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=ff4d5beb6ce1809d, https://usegalaxy.org.au/published/workflow?id=0a3fb089674de144, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1641?version=1 |
assembly/ERGA-post-assembly-QC, genome-annotation/functional, genome-annotation/gene-centric, sequence-analysis/ncbi-blast-against-the-madland |
True |
False |
|
disco |
disco |
txt, fasta |
DISCO is a overlap-layout-consensus (OLC) metagenome assembler |
2017-10-26 |
http://disco.omicsbio.org/ |
|
disco |
1.3 |
To update |
Metagenomics, Assembly |
Protein sequence analysis |
Protein sequence analysis |
Structure determination |
Structure determination |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco |
disco |
DISCO |
DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. |
|
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
127 |
163 |
280 |
453 |
406 |
435 |
1525 |
1690 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2143 |
1805 |
598 |
533 |
|
|
True |
False |
|
dose_response_analysis_tool |
dr_curve |
jpg, tabular |
A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses |
2024-04-06 |
https://github.com/bernt-matthias/mb-galaxy-tools |
3.0.1 |
r-drc |
3.0_1 |
To update |
Ecology |
|
|
|
|
ufz |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
dram |
dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer |
fasta, gff3, tabular, genbank, xlsx, html |
DRAM for distilling microbial metabolism to automate the curation of microbiome function |
2022-09-01 |
https://github.com/WrightonLabCSU/DRAM |
1.5.0 |
dram |
1.5.0 |
Up-to-date |
Metagenomics |
Gene functional annotation |
Gene functional annotation |
Metagenomics, Biological databases, Molecular genetics |
Metagenomics, Biological databases, Molecular genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram |
dram |
DRAM |
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes |
|
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
0 |
120 |
120 |
13633 |
13633 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13633 |
13633 |
120 |
120 |
|
|
True |
False |
|
drep |
drep_compare, drep_dereplicate |
|
dRep compares and dereplicates genome sets |
2020-01-06 |
https://github.com/MrOlm/drep |
3.6.2 |
drep |
3.6.2 |
Up-to-date |
Metagenomics |
Genome comparison |
Genome comparison |
Metagenomics, Genomics, Sequence analysis |
Metagenomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep |
drep |
dRep |
Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
0 |
113 |
115 |
1708 |
1749 |
13 |
13 |
47 |
47 |
0 |
0 |
0 |
0 |
38 |
38 |
1273 |
1273 |
3069 |
3028 |
166 |
164 |
https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://workflowhub.eu/workflows/1352?version=4 |
genome-annotation/bacterial-genome-quality-control, microbiome/mags-building, microbiome/metagenomics-binning |
True |
False |
|
ectyper |
ectyper |
tabular, txt |
EC-Typer - in silico serotyping of Escherichia coli species |
2018-12-21 |
https://github.com/phac-nml/ecoli_serotyping |
2.0.0 |
ectyper |
2.0.0 |
Up-to-date |
Sequence Analysis |
Sequence assembly, Read pre-processing, Variant calling |
Sequence assembly, Read pre-processing, Variant calling |
Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows |
Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows |
nml |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper |
ectyper |
ECTyper |
Ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats. (Galaxy Version 1.0.0) |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
218 |
218 |
30463 |
30463 |
1 |
1 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
30473 |
30473 |
219 |
219 |
https://usegalaxy.eu/published/workflow?id=b90585626a793502 |
|
True |
False |
|
effectivet3 |
effectiveT3 |
tabular |
Find bacterial type III effectors in protein sequences |
2013-04-30 |
http://effectors.org |
0.0.21 |
effectiveT3 |
1.0.1 |
To update |
Sequence Analysis |
Sequence classification |
Sequence classification |
Sequence analysis |
Sequence analysis |
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 |
effectivet3 |
EffectiveT3 |
Prediction of putative Type-III secreted proteins. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
eggnog_mapper |
eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search |
|
eggnog-mapper fast functional annotation of novel sequences |
2019-11-11 |
https://github.com/eggnogdb/eggnog-mapper |
2.1.13 |
eggnog-mapper |
2.1.13 |
Up-to-date |
Proteomics |
Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval |
Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval |
Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis |
Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper |
eggnog-mapper-v2 |
eggNOG-mapper v2 |
EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. |
|
3 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
3 |
0 |
1977 |
2018 |
64994 |
65580 |
518 |
518 |
9634 |
9634 |
541 |
541 |
25986 |
25986 |
144 |
144 |
66224 |
66224 |
167424 |
166838 |
3221 |
3180 |
https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=2d2862b48918b22f, https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=972da31ce19c0beb, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c, https://usegalaxy.fr/published/workflow?id=20e1c40739fad57b, https://usegalaxy.fr/published/workflow?id=3b65122efecd004f, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb, https://usegalaxy.org/published/workflow?id=92613e1e0b13aa0a, https://usegalaxy.org/published/workflow?id=d3c400275889ce4b, https://workflowhub.eu/workflows/1262?version=1, https://workflowhub.eu/workflows/1521?version=1, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/2024?version=2, https://workflowhub.eu/workflows/754?version=1, https://workflowhub.eu/workflows/755?version=1 |
genome-annotation/funannotate, genome-annotation/functional |
True |
False |
|
emboss |
emboss_needle, emboss_needleall |
needle |
Galaxy wrappers for EMBOSS6 tools |
2025-01-17 |
http://emboss.open-bio.org/ |
6.6.0 |
emboss |
6.6.0 |
Up-to-date |
Sequence Analysis, Fasta Manipulation |
Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment |
Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment |
Molecular biology, Sequence analysis, Biology |
Molecular biology, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss |
emboss |
EMBOSS |
Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
62 |
62 |
419 |
419 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
419 |
419 |
62 |
62 |
|
|
True |
False |
|
emboss_5 |
EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 |
antigenic, txt, btwisted, cai, png, charge, checktrans, fasta, gff, chips, codcmp, coderet, compseq, cpgplot, cpgreport, cusp, dan, diffseq, digest, dreg, einverted, epestfind, table, equicktandem, est2genome, etandem, freak, fuzznuc, fuzzpro, fuzztran, garnier, geecee, motif, hmoment, isochore, markx0, simple, needle, newcpgreport, newcpgseek, noreturn, oddcomp, palindrome, dbmotif, pepcoil, pepinfo, pepstats, polydot, preg, prettyseq, primersearch, seqmatchall, showfeat, sixpack, supermatcher, syco, textsearch, seqtable, vectorstrip, srs, wobble, wordcount, match |
Galaxy wrappers for EMBOSS version 5.0.0 tools |
2017-01-11 |
http://emboss.open-bio.org/ |
5.0.0 |
emboss |
6.6.0 |
To update |
Sequence Analysis, Fasta Manipulation |
Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment |
Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment |
Molecular biology, Sequence analysis, Biology |
Molecular biology, Sequence analysis |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 |
emboss |
EMBOSS |
Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. |
|
107 |
107 |
107 |
107 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
107 |
0 |
0 |
0 |
107 |
107 |
107 |
0 |
444 |
513 |
264479 |
273772 |
1350 |
2518 |
169846 |
325994 |
557 |
810 |
29757 |
35329 |
51 |
51 |
997 |
1037 |
636132 |
465079 |
3892 |
2402 |
https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5, https://usegalaxy.eu/published/workflow?id=0ed8817a90caa2b1, https://usegalaxy.eu/published/workflow?id=1031e4c4f18e020e, https://usegalaxy.eu/published/workflow?id=1f88311a8e365c17, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=402b14906a03b2ef, https://usegalaxy.eu/published/workflow?id=6e1fe7372e93fae0, https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, https://usegalaxy.eu/published/workflow?id=9275d0c90a8713d6, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=a31100610fba17a1, https://usegalaxy.eu/published/workflow?id=ada52ba09b462567, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=b77e3b08092fa73e, https://usegalaxy.eu/published/workflow?id=d22dac11eba8c5a3, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.eu/published/workflow?id=eaf01ccb13aad3ec, https://usegalaxy.eu/published/workflow?id=eaf3c4d97399e673, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.fr/published/workflow?id=b3974acb70608e38, https://usegalaxy.org.au/published/workflow?id=203f9e69152fbb2a, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org.au/published/workflow?id=6b1b0a945d367b4c, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=b432a1312859edd2, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org.au/published/workflow?id=f21446cc44da50ce, https://usegalaxy.org/published/workflow?id=00381bbae3fd7e78, https://usegalaxy.org/published/workflow?id=17d9b233640aefec, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=3b37e1cb61ec6f8e, https://usegalaxy.org/published/workflow?id=3c7349268d74c576, https://usegalaxy.org/published/workflow?id=4884918895db9af0, https://usegalaxy.org/published/workflow?id=62316da77b1bfa5a, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=6b4ad51307a28c7f, https://usegalaxy.org/published/workflow?id=6f836f4b71d399e7, https://usegalaxy.org/published/workflow?id=8d8e8927d63803ef, https://usegalaxy.org/published/workflow?id=8e1c6ad6ff623015, https://usegalaxy.org/published/workflow?id=94da3d448bb8a137, https://usegalaxy.org/published/workflow?id=956987e628530c79, https://usegalaxy.org/published/workflow?id=a666aaaa32f62487, https://usegalaxy.org/published/workflow?id=cc6ee582a6e5cae2, https://usegalaxy.org/published/workflow?id=cdf5dffbed938d49, https://usegalaxy.org/published/workflow?id=d3a69b0b826331ef, https://usegalaxy.org/published/workflow?id=e1dcdc125122f561, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://usegalaxy.org/published/workflow?id=f737593a1db217c8, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1632?version=1, https://workflowhub.eu/workflows/1647?version=2, https://workflowhub.eu/workflows/2049?version=1, https://workflowhub.eu/workflows/439?version=4 |
sequence-analysis/viral_primer_design, variant-analysis/pox-tiled-amplicon, variant-analysis/tb-variant-analysis |
True |
False |
|
ete |
ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator |
tabular, sqlite, tsv, nhx |
Analyse phylogenetic trees using the ETE Toolkit |
2016-06-01 |
https://etetoolkit.org/ |
3.1.3 |
ete3 |
3.1.1 |
To update |
Phylogenetics |
Phylogenetic analysis, Phylogenetic tree editing |
Phylogenetic tree editing |
Phylogenetics |
Phylogenetics |
earlhaminst |
https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/ete |
https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/ete |
ete |
ete |
The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org |
|
0 |
0 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
0 |
30 |
39 |
279 |
1030 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
13 |
13 |
1043 |
292 |
41 |
32 |
|
|
True |
False |
|
ete_treeviewer |
ete_treeviewer |
svg |
A toolkit for the analysis and visualization of trees. |
2024-11-25 |
http://etetoolkit.org |
3.1.3 |
curl |
|
To update |
Phylogenetics |
Phylogenetic analysis, Phylogenetic tree editing |
Phylogenetic tree editing |
Phylogenetics |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit |
ete |
ete |
The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
130 |
130 |
1626 |
1626 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
5 |
5 |
1631 |
1631 |
134 |
134 |
https://workflowhub.eu/workflows/1650?version=1 |
sequence-analysis/tapscan-streptophyte-algae |
True |
False |
|
eukcc |
eukcc_single |
tabular |
Galaxy wrapper for EukCC |
2025-07-25 |
https://github.com/EBI-Metagenomics/EukCC |
2.1.3 |
eukcc |
2.1.3 |
Up-to-date |
Metagenomics |
Sequence assembly validation |
Sequence assembly validation |
Metagenomics |
Metagenomics |
ufz |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/eukcc |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/eukcc |
eukcc |
EukCC |
EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
eukrep |
eukrep |
fasta, txt |
Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets |
2025-07-30 |
https://github.com/patrickwest/EukRep |
0.6.7 |
eukrep |
0.6.7 |
Up-to-date |
Metagenomics |
Nucleic acid sequence analysis |
Nucleic acid sequence analysis |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/eukrep |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/eukrep |
eukrep |
EukRep |
Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
export2graphlan |
export2graphlan |
txt |
export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn |
2017-03-03 |
https://bitbucket.org/CibioCM/export2graphlan/overview |
0.20 |
export2graphlan |
0.22 |
To update |
Metagenomics |
Conversion |
Conversion |
Taxonomy, Metabolomics, Biomarkers |
Taxonomy, Metabolomics, Biomarkers |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan |
export2graphlan |
export2graphlan |
export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
589 |
710 |
6276 |
7303 |
193 |
213 |
712 |
791 |
122 |
123 |
616 |
632 |
16 |
16 |
43 |
43 |
8769 |
7647 |
1062 |
920 |
https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c, https://usegalaxy.eu/published/workflow?id=c01ef8354b585a1f, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2 |
microbiome/metatranscriptomics, microbiome/metatranscriptomics-short |
True |
False |
|
ez_histograms |
ez_histograms |
pdf, tabular |
ggplot2 histograms and density plots |
2024-02-07 |
https://github.com/tidyverse/ggplot2 |
3.4.4 |
r-ggplot2 |
2.2.1 |
To update |
Visualization, Statistics |
Data analysis, Statistical calculation, Visualisation |
Statistical calculation, Visualisation |
Ecology |
Ecology |
artbio |
https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms |
https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms |
ez_histograms |
ez_histograms |
This tool produces histograms or density plots from any tabular datasets, using ggplot2.You may provide headerless tables as well as tables with column headers. Any non-numeric columns will be filtered out. Your first column may contains row names, but it will also work if your first column already corresponds to the numeric values of a variable. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
fairy |
fairy_cov, fairy_sketch |
tabular, bcsp |
Fast approximate contig coverage for metagenomic binning |
2024-12-20 |
https://github.com/bluenote-1577/fairy |
0.5.8 |
fairy |
0.5.8 |
Up-to-date |
Metagenomics |
Read binning, Sequence assembly validation |
Read binning, Sequence assembly validation |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy |
fairy |
fairy |
fast approximate contig coverage for metagenomic binningFairy computes multi-sample contig coverage for metagenome-assembled genome (MAG) binning.Fairy is used after metagenomic assembly and before binning. It can- Calculate coverage 100x-1000x faster than read alignment (e.g. BWA)- Give comparable bins for multi-sample binning (short read or nanopore reads)- Output formats that are compatible with MetaBAT2, MaxBin2, SemiBin2, and more |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
148 |
148 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
148 |
148 |
5 |
5 |
|
|
True |
False |
|
falco |
falco |
html, txt |
A high throughput sequence QC analysis tool |
2024-04-17 |
https://github.com/smithlabcode/falco/ |
1.2.4 |
falco |
1.2.5 |
To update |
Sequence Analysis |
Sequencing quality control, Visualisation, Read mapping |
Sequencing quality control, Visualisation, Read mapping |
Workflows, Mapping, Imaging |
Workflows, Mapping, Imaging |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco |
falco |
Falco |
A high-speed FastQC emulation for quality control of sequencing data. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
3878 |
3878 |
162045 |
162045 |
965 |
965 |
16492 |
16492 |
274 |
274 |
5029 |
5029 |
24 |
24 |
357 |
357 |
183923 |
183923 |
5141 |
5141 |
https://usegalaxy.eu/published/workflow?id=046e5c9726c75a3c, https://usegalaxy.eu/published/workflow?id=259f459a45e17e46, https://usegalaxy.eu/published/workflow?id=2d07557ce7703017, https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=4e2dc70a35ada981, https://usegalaxy.eu/published/workflow?id=6368019ffdf6c5ee, https://usegalaxy.eu/published/workflow?id=6f878d8b43ef1521, https://usegalaxy.eu/published/workflow?id=766f7099b5b1492a, https://usegalaxy.eu/published/workflow?id=79fa095c9fce9923, https://usegalaxy.eu/published/workflow?id=8b8e89b9b8801f2f, https://usegalaxy.eu/published/workflow?id=aa006065d085eb37, https://usegalaxy.eu/published/workflow?id=b144287d56b3291b, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=d17839eaeac6c4c8, https://usegalaxy.eu/published/workflow?id=d38f1f6a499a27fb, https://usegalaxy.eu/published/workflow?id=dec3f75e4496b26a, https://usegalaxy.eu/published/workflow?id=ece3ffe0800e6880, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=7cd1acb1da823cdc, https://usegalaxy.org/published/workflow?id=38f9fc867c4d1f40, https://usegalaxy.org/published/workflow?id=467d3e260c21de98, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1506?version=2, https://workflowhub.eu/workflows/1562?version=1, https://workflowhub.eu/workflows/1602?version=2, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1715?version=3, https://workflowhub.eu/workflows/1717?version=2, https://workflowhub.eu/workflows/1845?version=1, https://workflowhub.eu/workflows/2043?version=1 |
assembly/mrsa-illumina, ecology/ENA_Biodiv_submission, epigenetics/cut_and_run, epigenetics/methylation-seq, galaxy-interface/workflow-automation, galaxy-interface/workflow-fairification, sequence-analysis/quality-contamination-control, single-cell/scatac-preprocessing-tenx, transcriptomics/mirna-target-finder, transcriptomics/ref-based, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants |
True |
False |
|
fargene |
fargene |
txt, tar.gz |
fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) |
2019-08-30 |
https://github.com/fannyhb/fargene |
0.1 |
fargene |
0.1 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Metagenomics, Microbiology, Public health and epidemiology, Antimicrobial resistance |
Metagenomics, Microbiology, Public health and epidemiology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene |
fargene |
fARGene |
fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. |
|
1 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
150 |
159 |
895 |
1011 |
262 |
287 |
1203 |
1346 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
2359 |
2100 |
448 |
414 |
|
|
True |
False |
|
fastani |
fastani |
tabular |
Fast alignment-free computation of whole-genome Average Nucleotide Identity |
2020-02-17 |
https://github.com/ParBLiSS/FastANI |
1.3 |
fastani |
1.34 |
To update |
Sequence Analysis |
Genome alignment, Sequence similarity search |
Genome alignment, Sequence similarity search |
Microbiology, Genetic variation |
Microbiology, Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani |
fastani |
FastANI |
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1182 |
1205 |
29436 |
29626 |
1 |
1 |
18 |
18 |
133 |
133 |
1799 |
1799 |
64 |
64 |
949 |
949 |
32392 |
32202 |
1403 |
1380 |
https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75 |
|
True |
False |
|
fastk |
fastk_fastk, fastk_histex, fastk_logex |
fastk_ktab_tar, fastk_hist, fastk_ktab, txt, tabular |
FastK: A K-mer counter (for HQ assembly data sets) |
2024-05-03 |
https://github.com/thegenemyers/FASTK |
1.1.0 |
fastk |
1.2 |
To update |
Assembly |
k-mer counting, Sequence analysis |
k-mer counting, Sequence analysis |
Genomics, Sequence analysis |
Genomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk |
fastk |
FASTK |
FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode. |
|
3 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
46 |
46 |
742 |
742 |
45 |
45 |
389 |
389 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1131 |
1131 |
91 |
91 |
|
|
True |
False |
|
fastoma |
fastoma |
xml, html, ipynb, tabular, newick |
FastOMA is a scalable tool for orthology inference among many genomes. |
2025-12-26 |
https://github.com/dessimozlab/FastOMA |
0.5.1 |
|
|
To update |
Phylogenetics, Sequence Analysis |
Phylogenetic tree reconciliation, Protein sequence analysis, Genome comparison, Sequence clustering, Phylogenetic inference (from molecular sequences) |
Phylogenetic tree reconciliation, Protein sequence analysis, Genome comparison, Sequence clustering, Phylogenetic inference (from molecular sequences) |
Comparative genomics |
Comparative genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastoma |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastoma |
fastoma |
FastOMA |
FastOMA is a scalable software package to infer orthology relationship. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
fastp |
fastp |
html, json |
Fast all-in-one preprocessing for FASTQ files |
2018-03-07 |
https://github.com/OpenGene/fastp |
1.1.0 |
fastp |
1.1.0 |
Up-to-date |
Sequence Analysis |
Sequencing quality control, Sequence contamination filtering |
Sequence contamination filtering |
Sequence analysis, Probes and primers |
Probes and primers |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp |
fastp |
fastp |
A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
10510 |
10845 |
1229203 |
1372687 |
13972 |
14837 |
495065 |
537410 |
3030 |
3115 |
99990 |
109532 |
303 |
306 |
30703 |
30747 |
2050376 |
1854961 |
29103 |
27815 |
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https://workflowhub.eu/workflows/518?version=1, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/601?version=2, https://workflowhub.eu/workflows/68?version=1 |
assembly/assembly-with-preprocessing, assembly/largegenome, assembly/mrsa-illumina, assembly/mrsa-nanopore, ecology/eDNA-taxonomic-analysis, galaxy-interface/workflow-automation, introduction/galaxy-intro-ngs-data-managment, introduction/vsi_qc, microbiome/beer-data-analysis, microbiome/mgnify-amplicon, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/quality-contamination-control, transcriptomics/differential-isoform-expression, variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon, variant-analysis/sars-cov-2, variant-analysis/tb-variant-analysis |
True |
False |
|
fastplong |
fastplong |
html, json, fastq |
Fastplong is used for ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.). |
2025-05-06 |
https://github.com/OpenGene/fastplong |
0.4.1 |
fastplong |
0.4.1 |
Up-to-date |
Sequence Analysis, Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastplong |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastplong |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
40 |
40 |
309 |
309 |
0 |
0 |
0 |
0 |
8 |
8 |
217 |
217 |
0 |
0 |
0 |
0 |
526 |
526 |
48 |
48 |
https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3 |
|
True |
False |
|
fastqe |
fastqe |
html |
FASTQE |
2020-07-13 |
https://fastqe.com/ |
0.3.1+galaxy0 |
fastqe |
0.5.2 |
To update |
Sequence Analysis |
Sequencing quality control |
Sequencing quality control |
Sequence analysis, Sequencing |
Sequence analysis, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe |
fastqe |
FASTQE |
Compute quality stats for FASTQ files and print those stats as emoji... for some reason. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
3154 |
3177 |
6904 |
6978 |
6143 |
6198 |
13534 |
13627 |
1316 |
1323 |
3505 |
3549 |
291 |
291 |
510 |
510 |
24664 |
24453 |
10989 |
10904 |
https://usegalaxy.eu/published/workflow?id=055eae88be2d4dd7, https://usegalaxy.eu/published/workflow?id=2a274e0e4ba45c77, https://usegalaxy.eu/published/workflow?id=340aa3ae5468deb0, https://usegalaxy.eu/published/workflow?id=4c736e255f4a740f, https://usegalaxy.eu/published/workflow?id=519e0ffdfd1790bc, https://usegalaxy.eu/published/workflow?id=76a63b1710da5e60, https://usegalaxy.eu/published/workflow?id=a8d814a6d86e9661, https://usegalaxy.eu/published/workflow?id=c65d98740ca64104, https://usegalaxy.eu/published/workflow?id=d38f1f6a499a27fb, https://usegalaxy.eu/published/workflow?id=d3ae8c51061330f3, https://usegalaxy.eu/published/workflow?id=d5780c37232e3181, https://usegalaxy.org.au/published/workflow?id=115151c2c8998d44, https://usegalaxy.org.au/published/workflow?id=178db14511c8f293, https://usegalaxy.org.au/published/workflow?id=1f63ec596e578b1c, https://usegalaxy.org.au/published/workflow?id=2afeae1ec03c0b57, https://usegalaxy.org.au/published/workflow?id=43f2dabbc1932e30, https://usegalaxy.org.au/published/workflow?id=47cacc06d404a8c6, https://usegalaxy.org.au/published/workflow?id=5d6773ed5b2f41cb, https://usegalaxy.org.au/published/workflow?id=8fe84de499e96485, https://usegalaxy.org.au/published/workflow?id=bd251174d94cde9d, https://usegalaxy.org.au/published/workflow?id=dd6f465ab1eb10b0, https://usegalaxy.org.au/published/workflow?id=e08b04291839e79a, https://usegalaxy.org/published/workflow?id=20da2dcce0ae2ca2, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=cf2dbc29ca20ebee, https://usegalaxy.org/published/workflow?id=fe262214fba1cb8e |
sequence-analysis/quality-control |
True |
False |
|
fastreer |
fastreer_dist2tree, fastreer_fasta2dist, fastreer_vcf2dist, fastreer_vcf2tree |
newick, txt |
fastreeR toolkit wrappers for phylogenetic trees and distance matrices from VCF and FASTA |
2025-11-01 |
https://github.com/gkanogiannis/fastreeR |
2.1.2 |
fastreer |
2.1.3 |
To update |
Phylogenetics, Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastreer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastreer |
fastreer |
|
|
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
fastspar |
fastspar, fastspar_pvalues, fastspar_reduce |
tabular |
Tool for rapid and scalable correlation estimation for compositional data. |
2025-06-16 |
https://github.com/scwatts/fastspar/ |
1.0.0 |
fastspar |
1.0.0 |
Up-to-date |
Metagenomics, Statistics |
|
|
Metagenomics, Microbial ecology |
Metagenomics, Microbial ecology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastspar |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastspar |
FastSpar |
FastSpar |
FastSpar is a C++ implementation of the SparCC algorithm for fast correlation estimation from compositional count data such as microbiome OTU tables. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1 |
|
|
True |
False |
|
fasttree |
fasttree |
nhx, txt |
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL |
2018-02-02 |
http://www.microbesonline.org/fasttree/ |
2.1.10 |
fasttree |
2.2.0 |
To update |
Phylogenetics |
Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) |
|
Phylogenetics, Sequence analysis |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree |
fasttree |
FastTree |
Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1826 |
1923 |
84447 |
85175 |
2879 |
3069 |
29857 |
32881 |
829 |
967 |
8573 |
9437 |
82 |
84 |
411 |
416 |
127909 |
123288 |
6043 |
5616 |
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evolution/abc_intro_phylo, evolution/bacterial-comparative-genomics, microbiome/pathogen-detection-from-nanopore-foodborne-data |
True |
False |
|
featurecounts |
featurecounts |
tabular, bam |
featureCounts counts the number of reads aligned to defined masked regions in a reference genome |
2016-02-09 |
https://subread.sourceforge.net/ |
2.1.1 |
subread |
2.1.1 |
Up-to-date |
RNA, Transcriptomics, Sequence Analysis |
Read summarisation, RNA-Seq quantification |
Read summarisation, RNA-Seq quantification |
RNA-Seq |
RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts |
featurecounts |
FeatureCounts |
featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. |
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1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
14615 |
16504 |
807686 |
914668 |
26510 |
33788 |
760980 |
995817 |
2872 |
3227 |
79521 |
90365 |
1581 |
1583 |
52228 |
52279 |
2053129 |
1700415 |
55102 |
45578 |
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single-cell/scrna-preprocessing, transcriptomics/de-novo, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts |
True |
False |
|
filter_spades_repeats |
filter_spades_repeat |
fasta, txt |
Remove short and repeat contigs/scaffolds |
2017-10-12 |
https://github.com/phac-nml/galaxy_tools/ |
1.0.1 |
perl-bioperl |
1.7.8 |
To update |
Assembly |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools/ |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
filtlong |
filtlong |
fastqsanger |
Filtlong - Filtering long reads by quality |
2018-09-14 |
https://github.com/rrwick/Filtlong |
0.3.1 |
filtlong |
0.3.1 |
Up-to-date |
Fastq Manipulation, Sequence Analysis |
Filtering, Sequencing quality control |
Filtering, Sequencing quality control |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong |
filtlong |
Filtlong |
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
2169 |
2318 |
79820 |
82849 |
1410 |
1424 |
72145 |
72255 |
830 |
830 |
17538 |
17538 |
27 |
27 |
150 |
150 |
172792 |
169653 |
4599 |
4436 |
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assembly/mrsa-nanopore |
True |
False |
|
flashlfq |
flashlfq |
txt, tabular |
FlashLFQ mass-spectrometry proteomics label-free quantification |
2017-12-06 |
https://github.com/smith-chem-wisc/FlashLFQ |
1.0.3.1 |
flashlfq |
2.1.4 |
To update |
Proteomics |
Label-free quantification |
Label-free quantification |
Proteomics experiment, Proteomics |
Proteomics experiment, Proteomics |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq |
flashlfq |
FlashLFQ |
FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
47 |
59 |
516 |
760 |
0 |
0 |
0 |
0 |
16 |
16 |
216 |
226 |
0 |
0 |
0 |
0 |
986 |
732 |
75 |
63 |
https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://workflowhub.eu/workflows/1450?version=1 |
proteomics/metaquantome-data-creation |
True |
False |
|
flye |
flye |
fasta, graph_dot, gfa1, tabular, txt |
Assembly of long and error-prone reads. |
2018-09-22 |
https://github.com/fenderglass/Flye/ |
2.9.6 |
flye |
2.9.6 |
Up-to-date |
Assembly |
Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly |
Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly |
Sequence assembly, Metagenomics, Whole genome sequencing, Genomics |
Sequence assembly, Metagenomics, Whole genome sequencing |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/flye |
https://github.com/bgruening/galaxytools/tree/master/tools/flye |
Flye |
Flye |
Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
4818 |
4961 |
49679 |
51133 |
4110 |
4110 |
36053 |
36053 |
2250 |
2274 |
13882 |
14419 |
185 |
185 |
1088 |
1088 |
102693 |
100702 |
11530 |
11363 |
https://usegalaxy.eu/published/workflow?id=0ebfab0e957b7267, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=30b514cfb9cce524, https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef, https://usegalaxy.eu/published/workflow?id=368d1ac0150ea0b6, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=77e5bbd317750915, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=9ddb703e1db13504, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=b1d9e56aef03672b, https://usegalaxy.eu/published/workflow?id=b2dfa74f55a73409, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=cf8591391a17a914, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.org.au/published/workflow?id=02c74095a7128c9d, https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060, https://usegalaxy.org.au/published/workflow?id=1ad4c47cee851dda, https://usegalaxy.org.au/published/workflow?id=22bd45f60c60a338, https://usegalaxy.org.au/published/workflow?id=2cb16d321a804b1a, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=479c6b0a96ea1610, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=5b32e2f0d390a4ba, https://usegalaxy.org.au/published/workflow?id=68f5c371adbe5490, https://usegalaxy.org.au/published/workflow?id=7c343e5b55474d19, https://usegalaxy.org.au/published/workflow?id=803ef29108e36e58, https://usegalaxy.org.au/published/workflow?id=8a40059343cf4b87, https://usegalaxy.org.au/published/workflow?id=b5403e4fff2961f9, https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248, https://usegalaxy.org.au/published/workflow?id=c4d23297f6fbf5f3, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=d832905fbaf2ca31, https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2, https://usegalaxy.org.au/published/workflow?id=fc664a96d8099652, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=0602c14704dbe1ff, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5, https://usegalaxy.org/published/workflow?id=48dafc35989f13b1, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=5626a440a5798458, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=bff206b4625375bc, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://usegalaxy.org/published/workflow?id=c8d74054c1820087, https://usegalaxy.org/published/workflow?id=cce88bc57b180d09, https://usegalaxy.org/published/workflow?id=cdcf91a8ddb5dcd1, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/1114?version=1, https://workflowhub.eu/workflows/1495?version=1, https://workflowhub.eu/workflows/1595?version=1, https://workflowhub.eu/workflows/1613?version=2, https://workflowhub.eu/workflows/1617?version=1, https://workflowhub.eu/workflows/1621?version=1, https://workflowhub.eu/workflows/2011?version=1, https://workflowhub.eu/workflows/225?version=1, https://workflowhub.eu/workflows/51?version=1, https://workflowhub.eu/workflows/750?version=3, https://workflowhub.eu/workflows/788?version=1 |
assembly/chloroplast-assembly, assembly/hifi-assembly, assembly/hybrid_denovo_assembly, assembly/largegenome, assembly/mrsa-nanopore, microbiome/pathogen-detection-from-nanopore-foodborne-data |
True |
False |
|
format_metaphlan2_output |
format_metaphlan2_output |
tabular |
Format MetaPhlAn2 output to extract abundance at different taxonomic levels |
2022-10-19 |
|
0.2.0 |
|
|
To update |
Metagenomics |
Formatting |
Formatting |
Taxonomy, Metagenomics |
Taxonomy, Metagenomics |
bebatut |
https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ |
https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output |
format_metaphlan2_output |
Format metaphlan2 output |
This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
555 |
731 |
6485 |
7678 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7678 |
6485 |
731 |
555 |
https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=c01ef8354b585a1f, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b |
|
True |
False |
|
fraggenescan |
fraggenescan |
tabular, fasta, gff |
Tool for finding (fragmented) genes in short read |
2017-09-04 |
https://sourceforge.net/projects/fraggenescan/ |
|
fraggenescan |
1.32 |
To update |
Sequence Analysis |
Gene prediction |
Gene prediction |
Genetics, Sequence analysis |
Genetics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan |
fraggenescan |
FragGeneScan |
Application for finding (fragmented) genes in short reads |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
160 |
193 |
1267 |
1643 |
0 |
0 |
0 |
0 |
48 |
48 |
1171 |
1208 |
2 |
2 |
12 |
12 |
2863 |
2450 |
243 |
210 |
https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=534f5fc25bc887ca, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=972da31ce19c0beb, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=d57d41e306241396 |
|
True |
False |
|
fragpipe |
fragpipe, fragpipe_manifest_generator |
txt, csv, tsv, tabular |
Data analysis for mass spectrometry-based proteomics. |
2022-07-21 |
https://fragpipe.nesvilab.org/ |
23.0 |
fragpipe |
24.0 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe |
|
|
|
|
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
41 |
41 |
435 |
435 |
23 |
23 |
70 |
70 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
505 |
505 |
64 |
64 |
https://usegalaxy.eu/published/workflow?id=4c7fabcb345f5990, https://usegalaxy.eu/published/workflow?id=8ef3379dded2490a, https://usegalaxy.eu/published/workflow?id=bee2a7669a7dea5b, https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85, https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e, https://workflowhub.eu/workflows/1410?version=1, https://workflowhub.eu/workflows/1793?version=1 |
proteomics/neoantigen-fragpipe-discovery |
True |
False |
|
freqsap |
freqsap |
tabular |
Get frequencies of single amino-acid polymorphisms based on nucleid-acid polymorphism for different populations from UniProt and DbSNP. |
2025-07-18 |
https://github.com/RECETOX/galaxytools |
1.0.0+galaxy0 |
pandas |
|
To update |
Proteomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/main/tools/freqsap |
https://github.com/RECETOX/galaxytools/tree/master/tools/freqsap |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
freyja |
freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants |
tabular, html, pdf, csv |
lineage abundances estimation |
2022-07-05 |
https://github.com/andersen-lab/Freyja |
2.0.1 |
freyja |
2.0.3 |
To update |
Metagenomics, Sequence Analysis |
RNA-Seq quantification |
RNA-Seq quantification |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja |
freyja |
Freyja |
Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset |
|
2 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
58 |
58 |
24576 |
24576 |
15 |
15 |
327 |
327 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
24903 |
24903 |
73 |
73 |
https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b |
|
True |
False |
|
frogs_core |
FROGS_Core_Companion, FROGS_Core_Main |
|
Suite for metabarcoding analysis |
2025-07-25 |
http://frogs.inrae.fr/ |
5.1.0 |
|
|
To update |
Metagenomics |
|
|
|
|
frogs |
https://github.com/geraldinepascal/FROGS-wrappers/ |
https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs_core |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
frogs_func |
FROGS_Func |
|
Suite for metabarcoding analysis |
2025-08-27 |
http://frogs.inrae.fr/ |
5.1.0 |
|
|
To update |
Metagenomics |
|
|
|
|
frogs |
https://github.com/geraldinepascal/FROGS-wrappers/ |
https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs_func |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
frogs_stat |
FROGS_Stat |
|
Suite for metabarcoding analysis |
2025-07-23 |
http://frogs.inrae.fr/ |
5.1.0 |
|
|
To update |
Metagenomics |
|
|
|
|
frogs |
https://github.com/geraldinepascal/FROGS-wrappers/ |
https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs_stat |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
funannotate |
funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort |
genbank, tabular, fasta, txt, gff3, json, html |
Funannotate is a genome prediction, annotation, and comparison software package. |
2021-08-26 |
https://funannotate.readthedocs.io |
1.8.17 |
|
|
To update |
Genome annotation |
Genome annotation |
Genome annotation |
Genomics |
Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate |
funannotate |
funannotate |
funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). |
|
3 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
0 |
0 |
891 |
891 |
14118 |
14118 |
209 |
209 |
1453 |
1453 |
310 |
310 |
8597 |
8597 |
88 |
88 |
1505 |
1505 |
25673 |
25673 |
1498 |
1498 |
https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=07c92110c3fffcf8, https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://usegalaxy.org.au/published/workflow?id=52065a4100b11184, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/754?version=1 |
ecology/phylogeny-data-prep, genome-annotation/funannotate |
True |
False |
|
gamma |
gamma_s, gamma |
tabular, gff, fasta |
Gene Allele Mutation Microbial Assessment |
2025-08-06 |
https://github.com/rastanton/GAMMA |
2.2 |
GAMMA |
2.2 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gamma |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gamma |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
genomad |
genomad_end_to_end |
|
Identify virus and plasmid genomes from nucleotide sequences |
2024-06-17 |
https://github.com/apcamargo/genomad/ |
1.11.1 |
genomad |
1.11.2 |
To update |
Metagenomics |
Sequence annotation, Taxonomic classification |
Sequence annotation, Taxonomic classification |
Sequence analysis |
Sequence analysis |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad |
genomad |
geNomad |
geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes. |
|
1 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
119 |
119 |
2576 |
2576 |
20 |
20 |
71 |
71 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2647 |
2647 |
139 |
139 |
https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 |
|
True |
False |
|
getmlst |
getmlst |
fasta, tabular |
Download MLST datasets by species from pubmlst.org |
2015-12-03 |
|
0.1.4.1 |
srst2 |
0.2.0 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
gfastats |
gfastats |
tabular, fastq |
Tool for generating sequence statistics and simultaneous genome assembly file manipulation. |
2022-03-08 |
https://github.com/vgl-hub/gfastats |
1.3.11 |
gfastats |
1.3.11 |
Up-to-date |
Sequence Analysis |
Data handling |
Data handling |
Computational biology |
Computational biology |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/gfastats |
https://github.com/bgruening/galaxytools/tree/master/tools/gfastats |
gfastats |
gfastats |
gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
1105 |
1105 |
19582 |
19582 |
735 |
735 |
15352 |
15352 |
183 |
183 |
4128 |
4128 |
5 |
5 |
453 |
453 |
39515 |
39515 |
2028 |
2028 |
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https://workflowhub.eu/workflows/642?version=25, https://workflowhub.eu/workflows/643?version=5, https://workflowhub.eu/workflows/645?version=16, https://workflowhub.eu/workflows/701?version=1, https://workflowhub.eu/workflows/702?version=1, https://workflowhub.eu/workflows/751?version=19, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1 |
assembly/ERGA-post-assembly-QC, assembly/assembly-decontamination, assembly/vgp_genome_assembly |
True |
False |
|
gi2taxonomy |
Fetch Taxonomic Ranks |
taxonomy |
Fetch taxonomic representation |
2014-01-27 |
https://bitbucket.org/natefoo/taxonomy |
1.1.1 |
taxonomy |
0.10.2 |
To update |
Metagenomics |
Database search, ID mapping |
Database search, ID mapping |
Taxonomy |
Taxonomy |
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy |
gi2taxonomy |
gi2taxonomy |
The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
68 |
116 |
244 |
713 |
17 |
1798 |
113 |
14058 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
6 |
14777 |
357 |
1915 |
85 |
https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c |
|
True |
False |
|
glimmer_hmm |
|
|
GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) |
2015-02-28 |
https://ccb.jhu.edu/software/glimmerhmm/ |
|
|
|
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm |
https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
goenrichment |
goenrichment, goslimmer |
tabular, png |
Performs GO Enrichment analysis. |
2018-12-28 |
https://github.com/DanFaria/GOEnrichment |
2.0.1 |
goenrichment |
2.0.1 |
Up-to-date |
Genome annotation |
Gene-set enrichment analysis |
Gene-set enrichment analysis |
Transcriptomics |
Transcriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment |
goenrichment |
GOEnrichment |
GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
0 |
799 |
928 |
6000 |
7557 |
1081 |
1196 |
8060 |
9309 |
230 |
233 |
1602 |
1647 |
5 |
6 |
39 |
44 |
18557 |
15701 |
2363 |
2115 |
https://usegalaxy.eu/published/workflow?id=5f053303601cc630, https://usegalaxy.eu/published/workflow?id=7136ce9f18c74853, https://usegalaxy.org.au/published/workflow?id=d04b26372b28e8ed, https://workflowhub.eu/workflows/1515?version=1, https://workflowhub.eu/workflows/1667?version=1 |
single-cell/GO-enrichment, transcriptomics/goenrichment |
True |
False |
|
goseq |
goseq |
tabular, pdf, rdata |
goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data |
2016-11-12 |
https://bioconductor.org/packages/release/bioc/html/goseq.html |
1.50.0 |
bioconductor-goseq |
1.58.0 |
To update |
Statistics, RNA, Micro-array Analysis |
Gene functional annotation |
Gene functional annotation |
RNA-Seq |
RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq |
goseq |
GOseq |
Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
3196 |
3921 |
23708 |
28273 |
3528 |
4089 |
26762 |
31254 |
640 |
680 |
4461 |
5015 |
103 |
104 |
751 |
784 |
65326 |
55682 |
8794 |
7467 |
https://usegalaxy.eu/published/workflow?id=032ad839dab7ae70, https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=c1a6d11e1eab6a42, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.org.au/published/workflow?id=4f0814ec9f9f8425, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=420a332da24fb9e9, https://usegalaxy.org/published/workflow?id=742120336d5ff997, https://workflowhub.eu/workflows/1194?version=1, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1699?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=2, https://workflowhub.eu/workflows/689?version=1 |
transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways |
True |
False |
|
graphlan |
graphlan, graphlan_annotate |
png, pdf, ps, eps, svg, phyloxml |
GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees |
2017-03-03 |
https://github.com/biobakery/graphlan |
|
graphlan |
1.1.3 |
To update |
Metagenomics, Graphics, Phylogenetics |
Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification |
Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification |
Metagenomics, Phylogenetics, Phylogenomics, Cladistics |
Metagenomics, Phylogenetics, Phylogenomics, Cladistics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan |
graphlan |
GraPhlAn |
GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
0 |
799 |
940 |
11872 |
13928 |
325 |
325 |
1773 |
1773 |
202 |
207 |
1432 |
1470 |
21 |
21 |
90 |
90 |
17261 |
15167 |
1493 |
1347 |
https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c, https://usegalaxy.eu/published/workflow?id=c01ef8354b585a1f, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2 |
microbiome/metatranscriptomics, microbiome/metatranscriptomics-short |
True |
False |
|
groot |
groot |
tabular |
GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples |
2024-05-14 |
https://github.com/will-rowe/groot |
1.1.2 |
groot |
1.1.2 |
Up-to-date |
Metagenomics |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Metagenomics, Microbiology, Genomics |
Metagenomics, Microbiology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot |
groot |
GROOT |
Indexed variation graphs for efficient and accurate resistome profiling. |
|
1 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
5 |
5 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
37 |
37 |
44 |
44 |
8 |
8 |
https://workflowhub.eu/workflows/2068?version=1 |
|
True |
False |
|
gtdb_to_taxdump |
gtdb_to_taxdump |
tabular |
Convert GTDB taxonomy to NCBI taxdump format |
2024-08-25 |
https://github.com/nick-youngblut/gtdb_to_taxdump |
0.1.9 |
gtdb_to_taxdump |
0.1.9 |
Up-to-date |
Metagenomics |
Data handling, Mapping, Generation |
Data handling, Mapping, Generation |
Computational biology |
Computational biology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump |
gtdb_to_taxdump |
gtdb_to_taxdump |
Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. |
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
27 |
27 |
1127 |
1127 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1127 |
1127 |
27 |
27 |
https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1 |
|
True |
False |
|
gtdbtk |
gtdbtk_classify_wf |
txt |
GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. |
2022-12-13 |
https://github.com/Ecogenomics/GTDBTk |
2.6.1 |
gtdbtk |
2.6.1 |
Up-to-date |
Metagenomics |
Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval |
Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval |
Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins |
Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk |
GTDB-Tk |
GTDB-Tk |
a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
462 |
462 |
3982 |
3982 |
305 |
305 |
1566 |
1566 |
177 |
177 |
1095 |
1095 |
15 |
15 |
1439 |
1439 |
8082 |
8082 |
959 |
959 |
https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://workflowhub.eu/workflows/1352?version=4 |
|
True |
False |
|
gubbins |
gubbins |
txt, gff3, embl, fasta, phylip, csv, vcf |
Gubbins - bacterial recombination detection |
2017-06-22 |
|
3.2.1 |
gubbins |
3.4.3 |
To update |
Sequence Analysis |
Genotyping, Phylogenetic inference, Ancestral reconstruction |
Genotyping, Phylogenetic inference, Ancestral reconstruction |
Phylogeny, Genotype and phenotype, Whole genome sequencing |
Phylogeny, Genotype and phenotype, Whole genome sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins |
gubbins |
Gubbins |
Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. |
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
402 |
428 |
4731 |
5118 |
268 |
288 |
3847 |
4061 |
250 |
317 |
1977 |
2858 |
0 |
0 |
0 |
0 |
12037 |
10555 |
1033 |
920 |
|
|
True |
False |
|
guppy_basecaller |
guppy-basecaller |
fastqsanger, txt |
A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies |
2020-11-18 |
http://artbio.fr |
6.5.7+galaxy0 |
|
|
To update |
Nanopore |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy |
https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
7 |
7 |
0 |
0 |
0 |
0 |
7 |
7 |
1 |
1 |
|
|
True |
False |
|
halla |
halla |
tabular, pdf |
Hierarchical All-against-All association |
2025-11-05 |
https://github.com/biobakery/halla |
0.8.40 |
halla |
0.8.40 |
Up-to-date |
Metagenomics |
Statistical calculation, Gene expression profiling, Essential dynamics |
Statistical calculation, Gene expression profiling, Essential dynamics |
Microbial ecology, Microarray experiment, Metabolomics, Phylogeny, Epigenetics |
Microbial ecology, Microarray experiment, Metabolomics, Phylogeny, Epigenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/halla |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/halla |
halla |
HAllA |
High-sensitivity pattern discovery in large, paired multi-omic datasets. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
hamronization |
hamronize_summarize, hamronize_tool |
tabular |
Convert AMR gene detection tool output to hAMRonization specification format. |
2021-02-02 |
https://github.com/pha4ge/hAMRonization |
1.1.4 |
hamronization |
1.1.9 |
To update |
Sequence Analysis |
Data handling, Antimicrobial resistance prediction, Parsing |
Antimicrobial resistance prediction, Parsing |
Public health and epidemiology, Microbiology, Bioinformatics |
Public health and epidemiology, Microbiology, Bioinformatics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization |
hamronization |
hAMRonization |
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
254 |
254 |
18459 |
18459 |
1 |
1 |
20 |
20 |
1 |
1 |
21 |
21 |
6 |
6 |
191 |
191 |
18691 |
18691 |
262 |
262 |
https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 |
|
True |
False |
|
hifiasm_meta |
hifiasm_meta |
|
A hifiasm fork for metagenome assembly using Hifi reads. |
2023-01-18 |
https://github.com/xfengnefx/hifiasm-meta |
0.3.1 |
hifiasm_meta |
hamtv0.3.1 |
To update |
Metagenomics |
Sequence assembly |
Sequence assembly |
Sequence assembly, Metagenomics |
Sequence assembly, Metagenomics |
galaxy-australia |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta |
hifiasm-meta |
Hifiasm-meta |
Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
40 |
40 |
229 |
229 |
0 |
0 |
0 |
0 |
16 |
16 |
368 |
368 |
0 |
0 |
0 |
0 |
597 |
597 |
56 |
56 |
|
|
True |
False |
|
hivtrace |
hivtrace |
txt |
An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. |
2015-12-10 |
|
1.0.1 |
hivtrace |
1.5.0 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
hmmer3 |
hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer |
stockholm, hmm3, fasta |
HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). |
2015-02-16 |
http://hmmer.org/ |
3.4 |
hmmer |
3.4 |
Up-to-date |
Sequence Analysis |
Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search |
Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search |
Sequence analysis, Sequence sites, features and motifs, Gene and protein families |
Sequence analysis, Sequence sites, features and motifs, Gene and protein families |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 |
hmmer3 |
HMMER3 |
This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. |
|
12 |
12 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
12 |
0 |
380 |
403 |
36302 |
43262 |
0 |
0 |
0 |
0 |
83 |
84 |
4731 |
4887 |
97 |
97 |
540 |
543 |
48692 |
41573 |
584 |
560 |
https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 |
|
True |
False |
|
humann |
humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways |
tabular, biom1, txt, sam, fasta, png, pdf, svg |
HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution |
2021-05-12 |
http://huttenhower.sph.harvard.edu/humann |
3.9 |
humann |
3.9 |
Up-to-date |
Metagenomics |
Species frequency estimation, Taxonomic classification, Phylogenetic analysis |
Species frequency estimation, Taxonomic classification, Phylogenetic analysis |
Metagenomics, Phylogenomics |
Metagenomics, Phylogenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann |
humann |
humann |
HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” |
|
6 |
10 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
0 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
10 |
10 |
0 |
795 |
795 |
52483 |
52483 |
123 |
123 |
3171 |
3171 |
122 |
122 |
4812 |
4812 |
17 |
17 |
987 |
987 |
61453 |
61453 |
1057 |
1057 |
https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=23dd2253da51e22e, https://usegalaxy.eu/published/workflow?id=3118d383c81cf805, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.fr/published/workflow?id=fd733565098d76c9, https://workflowhub.eu/workflows/1447?version=2, https://workflowhub.eu/workflows/1456?version=2, https://workflowhub.eu/workflows/1466?version=2 |
microbiome/metatranscriptomics, microbiome/metatranscriptomics-short |
True |
False |
|
hyphy |
hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_cln, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs |
markdown, hyphy_results.json, nhx, nex, fasta |
Hypothesis Testing using Phylogenies |
2018-06-08 |
http://www.hyphy.org |
2.5.93 |
hyphy |
2.5.93 |
Up-to-date |
Phylogenetics |
Statistical calculation |
Statistical calculation |
Phylogeny, Small molecules, Molecular interactions, pathways and networks |
Phylogeny, Small molecules, Molecular interactions, pathways and networks |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy |
HyPhy |
HyPhy |
Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. |
|
16 |
2 |
16 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
12 |
16 |
12 |
0 |
88 |
94 |
10953 |
11906 |
78 |
108 |
4725 |
8358 |
33 |
42 |
815 |
909 |
3 |
5 |
22 |
27 |
21200 |
16515 |
249 |
202 |
https://usegalaxy.eu/published/workflow?id=1d40d6deb2da04cc, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e |
|
True |
False |
|
hypo |
hypo |
fasta, txt |
Super Fast & Accurate Polisher for Long Read Genome Assemblies |
2021-11-15 |
https://github.com/kensung-lab/hypo |
1.0.3 |
hypo |
1.0.3 |
Up-to-date |
Assembly |
Optimisation and refinement, Genome assembly |
Optimisation and refinement, Genome assembly |
Sequence assembly, Genomics |
Sequence assembly, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo |
HyPo |
HyPo |
HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
107 |
107 |
575 |
575 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
575 |
575 |
107 |
107 |
https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1 |
|
True |
False |
|
icescreen |
icescreen |
tabular, txt, genbank.gz, gff3.gz, embl.gz, tar.gz, gz |
identification of ICEs and IMEs in Bacillota genomes. |
2022-01-04 |
https://forgemia.inra.fr/ices_imes_analysis/icescreen |
1.3.3 |
icescreen |
1.3.3 |
Up-to-date |
Genome annotation |
Database search, Protein feature detection |
Database search, Protein feature detection |
Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation |
Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen |
icescreen |
ICEscreen |
A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. |
|
1 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
153 |
153 |
4 |
4 |
15 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
168 |
168 |
7 |
7 |
|
|
True |
False |
|
idba |
idba_hybrid, idba_tran, idba_ud |
fasta |
Wrappers for the idba assembler variants. |
2018-04-26 |
https://i.cs.hku.hk/~alse/hkubrg/projects/index.html |
|
idba |
1.1.3 |
To update |
Assembly |
Sequence assembly |
Sequence assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud |
idba |
IDBA |
A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. |
|
3 |
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
0 |
106 |
126 |
944 |
1353 |
146 |
169 |
1199 |
1700 |
0 |
0 |
0 |
0 |
1 |
1 |
3 |
3 |
3056 |
2146 |
296 |
253 |
|
|
True |
False |
|
instrain |
instrain_compare, instrain_profile |
tabular, pdf, zip |
InStrain is a tool for analysis of co-occurring genome populations from metagenomes |
2021-08-11 |
https://instrain.readthedocs.io/ |
1.5.3 |
instrain |
1.10.0 |
To update |
Metagenomics |
SNP detection, Genome comparison |
SNP detection, Genome comparison |
Mapping, Metagenomics |
Mapping, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain |
instrain |
InStrain |
InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
22 |
22 |
208 |
208 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
208 |
208 |
22 |
22 |
|
|
True |
False |
|
integronfinder |
integron_finder |
txt, tsv |
"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching" |
2022-09-22 |
https://github.com/gem-pasteur/Integron_Finder |
2.0.5 |
integron_finder |
2.0.6 |
To update |
Sequence Analysis |
Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation |
Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation |
Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis |
Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder |
integron_finder |
Integron Finder |
A tool to detect Integron in DNA sequences. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
390 |
390 |
64428 |
64428 |
252 |
252 |
7167 |
7167 |
132 |
132 |
12061 |
12061 |
34 |
34 |
2504 |
2504 |
86160 |
86160 |
808 |
808 |
https://usegalaxy.eu/published/workflow?id=1306ed083d91a852, https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=67ca17ab34b10772, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=13, https://workflowhub.eu/workflows/1513?version=1 |
genome-annotation/bacterial-genome-annotation |
True |
False |
|
interproscan |
interproscan |
tabular, xml, gff3, json |
Interproscan queries the interpro database and provides annotations. |
2021-11-15 |
http://www.ebi.ac.uk/Tools/pfa/iprscan5/ |
5.59-91.0 |
interproscan |
5.59_91.0 |
To update |
Sequence Analysis |
Sequence motif recognition, Protein feature detection |
Sequence motif recognition, Protein feature detection |
Gene and protein families, Sequence analysis |
Gene and protein families, Sequence analysis |
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan |
interproscan_ebi |
InterProScan (EBI) |
Scan sequences against the InterPro protein signature databases. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
2350 |
2550 |
44154 |
69658 |
486 |
486 |
3914 |
3914 |
799 |
804 |
13188 |
13204 |
144 |
144 |
9435 |
9435 |
96211 |
70691 |
3984 |
3779 |
https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=2d2862b48918b22f, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a95556ec171d405, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6, https://usegalaxy.fr/published/workflow?id=20e1c40739fad57b, https://usegalaxy.fr/published/workflow?id=3b65122efecd004f, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a, https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=92613e1e0b13aa0a, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://workflowhub.eu/workflows/1262?version=1, https://workflowhub.eu/workflows/1521?version=1, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/1663?version=1, https://workflowhub.eu/workflows/754?version=1, https://workflowhub.eu/workflows/755?version=1 |
ecology/marine_omics_bgc, genome-annotation/funannotate, genome-annotation/functional |
True |
False |
|
iphop |
iphop_predict |
csv |
Integrated Phage Host Prediction |
2024-10-14 |
https://bitbucket.org/srouxjgi/iphop/ |
1.3.3 |
iphop |
1.4.2 |
To update |
Metagenomics |
Sample comparison |
Sample comparison |
|
|
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop |
iphop |
iPHoP |
An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. |
|
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
26 |
26 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
26 |
26 |
9 |
9 |
https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 |
|
True |
False |
|
iprscan5 |
|
|
Interproscan queries the interpro database and provides annotations. |
2015-02-28 |
http://www.ebi.ac.uk/Tools/pfa/iprscan5/ |
|
|
|
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 |
https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
iqtree |
iqtree |
nhx, mldist, nex, iqtree, data, txt |
Efficient phylogenomic software by maximum likelihood |
2017-09-26 |
http://www.iqtree.org/ |
2.4.0 |
iqtree |
3.0.1 |
To update |
Phylogenetics |
Phylogenetic analysis, Sequence analysis |
Phylogenetic analysis, Sequence analysis |
Phylogenetics |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree |
iqtree |
iqtree |
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
2588 |
2695 |
44137 |
45132 |
2814 |
3035 |
34112 |
35898 |
1165 |
1337 |
16490 |
18756 |
17 |
17 |
229 |
229 |
100015 |
94968 |
7084 |
6584 |
https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.eu/published/workflow?id=d5cf994c03a60fa4, https://usegalaxy.eu/published/workflow?id=e97b938ca4723827, https://usegalaxy.org.au/published/workflow?id=3242ec69dec6e13f, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=78d8b738f5715a8a, https://usegalaxy.org/published/workflow?id=952b83e52f7d7cff, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1559?version=1, https://workflowhub.eu/workflows/1839?version=1, https://workflowhub.eu/workflows/359?version=1 |
evolution/abc_intro_phylo, sequence-analysis/tapscan-streptophyte-algae, variant-analysis/aiv-analysis |
True |
False |
|
irma |
irma |
txt |
Iterative Refinement Meta-Assembler (IRMA) is a tool to construct assembly of highly variable RNA viruses. |
2024-11-09 |
https://wonder.cdc.gov/amd/flu/irma/irma.html |
1.2.0 |
irma |
1.2.0 |
Up-to-date |
Sequence Analysis |
Mapping assembly |
Mapping assembly |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/irma |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/irma |
irma-virus |
IRMA |
Iterative Refinement Meta-Assembler for robust assembly, variant calling, and phasing of highly variable RNA virus sequencing data |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
16450 |
16450 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16450 |
16450 |
12 |
12 |
|
|
True |
False |
|
itsx |
itsx |
fasta, txt, tabular |
ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. |
2022-05-02 |
https://microbiology.se/software/itsx/ |
1.1.3 |
itsx |
1.1.3 |
Up-to-date |
Metagenomics |
Sequence feature detection |
Sequence feature detection |
Functional, regulatory and non-coding RNA, Microbiology |
Functional, regulatory and non-coding RNA, Microbiology |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/itsx |
https://github.com/bgruening/galaxytools/tree/master/tools/itsx |
ITSx |
ITSx |
TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
140 |
140 |
2878 |
2878 |
0 |
0 |
0 |
0 |
18 |
18 |
198 |
198 |
0 |
0 |
0 |
0 |
3076 |
3076 |
158 |
158 |
https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67 |
|
True |
False |
|
ivar |
ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants |
fasta, tabular, bam, vcf |
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing |
2020-03-21 |
https://github.com/andersen-lab/ivar |
1.4.4 |
ivar |
1.4.4 |
Up-to-date |
Sequence Analysis |
Primer removal |
Primer removal |
Virology |
Virology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar |
andersen-lab_ivar |
iVar |
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. |
|
5 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
5 |
5 |
5 |
0 |
1081 |
1087 |
1414011 |
1417441 |
1310 |
1330 |
147224 |
148408 |
374 |
379 |
43473 |
54915 |
19 |
19 |
7502 |
7502 |
1628266 |
1612210 |
2815 |
2784 |
https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=0be293debca8fb9b, https://usegalaxy.eu/published/workflow?id=0f6a7bd5362e4a2b, https://usegalaxy.eu/published/workflow?id=2573209308aaad23, https://usegalaxy.eu/published/workflow?id=2d9d4445a1871230, https://usegalaxy.eu/published/workflow?id=3f046b416b10b871, https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=40d2c7ac42bd5302, https://usegalaxy.eu/published/workflow?id=429ae28a178cd07c, https://usegalaxy.eu/published/workflow?id=45fc2dada84d251e, https://usegalaxy.eu/published/workflow?id=476db04368d5e90c, https://usegalaxy.eu/published/workflow?id=4b4bfc79205d83f1, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=4d97068a725c975c, https://usegalaxy.eu/published/workflow?id=4f40ae432d8a4259, https://usegalaxy.eu/published/workflow?id=529f30e894beacc2, 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variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon |
True |
False |
|
jbrowse |
jbrowse_to_standalone, jbrowse |
html |
JBrowse Genome Browser integrated as a Galaxy Tool |
2015-05-01 |
https://jbrowse.org |
1.16.11 |
jbrowse |
1.16.11 |
Up-to-date |
Sequence Analysis |
Genome visualisation |
Genome visualisation |
Genomics |
Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse |
jbrowse |
JBrowse |
Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. |
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6793 |
7423 |
26043 |
28614 |
7372 |
7751 |
22125 |
23288 |
3208 |
4288 |
18197 |
22221 |
299 |
300 |
1697 |
1712 |
75835 |
68062 |
19762 |
17672 |
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assembly/chloroplast-assembly, assembly/ecoli_comparison, genome-annotation/amr-gene-detection, genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short, genome-annotation/annotation-with-prokka, genome-annotation/apollo, genome-annotation/apollo-euk, genome-annotation/bacterial-genome-annotation, genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation, genome-annotation/funannotate, genome-annotation/helixer, sequence-analysis/mapping, sequence-analysis/sars-with-galaxy-on-anvil, variant-analysis/microbial-variants, variant-analysis/tb-variant-analysis, visualisation/jbrowse |
True |
False |
|
jbrowse2 |
jbrowse2 |
html |
JBrowse2 Genome Browser integrated as a Galaxy Tool |
2021-09-30 |
https://jbrowse.org |
3.7.0 |
jbrowse2 |
4.1.3 |
To update |
Sequence Analysis |
Genome visualisation, Structure visualisation, Pathway visualisation |
Genome visualisation, Structure visualisation, Pathway visualisation |
Mapping, Structural variation, Genomics, Gene structure, Sequence assembly |
Mapping, Structural variation, Genomics, Gene structure, Sequence assembly |
fubar |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse2 |
jbrowse_2 |
JBrowse 2 |
Modular genome browser with views of synteny and structural variation. |
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626 |
626 |
3765 |
3765 |
349 |
349 |
1248 |
1248 |
95 |
95 |
603 |
603 |
0 |
0 |
0 |
0 |
5616 |
5616 |
1070 |
1070 |
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epigenetics/formation_of_super-structures_on_xi, transcriptomics/ref-based |
True |
False |
|
jbrowse2 |
jbrowse2 |
html |
JBrowse2 Genome Browser integrated as a Galaxy Tool |
2024-06-04 |
https://jbrowse.org |
2.17.0 |
jbrowse2 |
4.1.3 |
To update |
Sequence Analysis |
Genome visualisation, Structure visualisation, Pathway visualisation |
Genome visualisation, Structure visualisation, Pathway visualisation |
Mapping, Structural variation, Genomics, Gene structure, Sequence assembly |
Mapping, Structural variation, Genomics, Gene structure, Sequence assembly |
fubar |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 |
https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 |
jbrowse_2 |
JBrowse 2 |
Modular genome browser with views of synteny and structural variation. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
626 |
626 |
3765 |
3765 |
349 |
349 |
1248 |
1248 |
95 |
95 |
603 |
603 |
0 |
0 |
0 |
0 |
5616 |
5616 |
1070 |
1070 |
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epigenetics/formation_of_super-structures_on_xi, transcriptomics/ref-based |
True |
False |
|
jellyfish |
jellyfish |
jellyfish, txt, fasta, tsv |
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA |
2021-04-07 |
https://github.com/gmarcais/Jellyfish |
|
kmer-jellyfish |
2.3.1 |
To update |
Assembly |
k-mer counting |
k-mer counting |
Sequence analysis, Genomics |
Sequence analysis, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish |
Jellyfish |
Jellyfish |
A command-line algorithm for counting k-mers in DNA sequence. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
369 |
369 |
4901 |
4901 |
0 |
0 |
0 |
0 |
87 |
87 |
1492 |
1492 |
35 |
35 |
1519 |
1519 |
7912 |
7912 |
491 |
491 |
https://usegalaxy.eu/published/workflow?id=bc32937d505135ab |
|
True |
False |
|
kaiju |
kaiju_addtaxonnames, kaiju_mergeoutputs, kaiju_kaiju, kaiju_kaiju2krona, kaiju_kaiju2table |
tabular |
taxonomic classification of high-throughput sequencing reads |
2025-04-22 |
https://github.com/bioinformatics-centre/kaiju |
1.10.1 |
kaiju |
1.10.1 |
Up-to-date |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju |
kaiju |
Kaiju |
Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses. |
|
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
|
|
True |
False |
|
kat_filter |
kat_@EXECUTABLE@ |
fastqsanger, tabular |
Filtering kmers or reads from a database of kmers hashes |
2017-03-13 |
|
2.3 |
kat |
2.4.2 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
khmer |
khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median |
oxlicg, csv, txt |
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more |
2015-03-24 |
https://khmer.readthedocs.org/ |
3.0.0a3 |
khmer |
3.0.0a3 |
Up-to-date |
Assembly, Next Gen Mappers |
Standardisation and normalisation, De-novo assembly |
Standardisation and normalisation, De-novo assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer |
khmer |
khmer |
khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. |
|
8 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
8 |
8 |
8 |
0 |
98 |
116 |
1572 |
2262 |
169 |
185 |
1179 |
1564 |
25 |
25 |
2179 |
2179 |
0 |
0 |
0 |
0 |
6005 |
4930 |
326 |
292 |
|
|
True |
False |
|
kleborate |
kleborate |
tabular |
Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) |
2022-09-09 |
https://github.com/katholt/Kleborate |
2.3.2 |
kleborate |
3.2.4 |
To update |
Metagenomics |
Multilocus sequence typing, Genome assembly, Virulence prediction |
Multilocus sequence typing, Genome assembly, Virulence prediction |
Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing |
Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate |
kleborate |
Kleborate |
Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
123 |
123 |
1479 |
1479 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1479 |
1479 |
123 |
123 |
|
|
True |
False |
|
kmer2stats |
kmer2stats |
tabular |
A tool for creating data files for statistics based on kmers |
2025-04-16 |
https://github.com/SantaMcCloud/kmer2stats |
1.0.1 |
kmer2stats |
1.0.1 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
310 |
310 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
310 |
310 |
8 |
8 |
|
|
True |
False |
|
kmetashot |
kmetashot |
|
an alignment-free taxonomic classifier based on k-mer/minimizer counting |
2025-12-18 |
https://github.com/gdefazio/kMetaShot |
2.0 |
kmetashot |
2.0 |
Up-to-date |
Metagenomics |
|
|
|
|
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmetashot |
https://github.com/bgruening/galaxytools/tree/master/tools/kmetashot |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
kmindex |
kmindex_build, kmindex_query |
kmindex, json |
Index and query k-mers from sequencing samples using Bloom filters |
2025-12-10 |
https://github.com/tlemane/kmindex |
0.6.0 |
kmindex |
0.6.0 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmindex |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmindex |
kmindex |
kmindex |
kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
kofamscan |
kofamscan |
txt, zip |
Gene function annotation tool based on KEGG Orthology and hidden Markov model |
2020-11-12 |
https://github.com/takaram/kofam_scan |
1.3.0 |
kofamscan |
1.3.0 |
Up-to-date |
Sequence Analysis |
Sequence analysis, Gene functional annotation |
Sequence analysis, Gene functional annotation |
Genomics, Structure analysis |
Genomics, Structure analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan |
kofamscan |
kofamscan |
KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
94 |
94 |
2904 |
2904 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
3 |
3 |
2907 |
2907 |
96 |
96 |
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|
True |
False |
|
kraken |
kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken |
tabular |
Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. |
2017-01-24 |
http://ccb.jhu.edu/software/kraken/ |
|
kraken |
1.1.1 |
To update |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Taxonomy, Metagenomics |
Taxonomy, Metagenomics |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken |
kraken |
Kraken |
System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. |
|
5 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
5 |
5 |
5 |
0 |
1452 |
1453 |
75318 |
75385 |
2535 |
4229 |
59050 |
144905 |
904 |
1133 |
38078 |
44609 |
114 |
114 |
3720 |
3720 |
268619 |
176166 |
6929 |
5005 |
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|
True |
False |
|
kraken2 |
kraken2 |
tabular |
Kraken2 for taxonomic designation. |
2019-03-05 |
http://ccb.jhu.edu/software/kraken/ |
2.17.1 |
kraken2 |
2.17.1 |
Up-to-date |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Taxonomy, Metagenomics, Microbial ecology, Microbiology |
Taxonomy, Metagenomics, Microbial ecology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 |
kraken2 |
kraken2 |
Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.Any assumption that Kraken’s raw read assignments can be directly translated into species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN), estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree. (Lu, Jennifer et al. “Bracken: estimating species abundance in metagenomics data.”) |
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1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
9806 |
9999 |
519669 |
530279 |
7561 |
7562 |
224146 |
224149 |
2412 |
2459 |
87806 |
88898 |
216 |
216 |
26628 |
26628 |
869954 |
858249 |
20236 |
19995 |
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assembly/assembly-decontamination, ecology/bacterial-isolate-species-contamination-checking, microbiome/beer-data-analysis, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling, sequence-analysis/quality-contamination-control, variant-analysis/tb-variant-analysis |
True |
False |
|
kraken2tax |
Kraken2Tax |
taxonomy |
Convert Kraken output to Galaxy taxonomy data. |
2015-08-05 |
https://bitbucket.org/natefoo/taxonomy |
1.2+galaxy0 |
gawk |
|
To update |
Metagenomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax |
|
|
|
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1365 |
1376 |
33158 |
33186 |
1892 |
2555 |
18299 |
28718 |
564 |
576 |
19721 |
19871 |
0 |
0 |
0 |
0 |
81775 |
71178 |
4507 |
3821 |
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|
True |
False |
|
kraken_biom |
kraken_biom |
tabular, mothur.map |
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) |
2022-09-03 |
https://github.com/smdabdoub/kraken-biom |
1.2.0 |
kraken-biom |
1.2.0 |
Up-to-date |
Metagenomics |
Genome annotation, Taxonomic classification |
Genome annotation, Taxonomic classification |
Metagenomics, Taxonomy |
Metagenomics, Taxonomy |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom |
kraken-biom |
kraken-biom |
Create BIOM-format tables from Kraken output |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
857 |
857 |
4747 |
4747 |
47 |
47 |
150 |
150 |
95 |
95 |
963 |
963 |
9 |
9 |
17 |
17 |
5877 |
5877 |
1008 |
1008 |
https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=a0ea6fc756dd17ea, https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962, https://workflowhub.eu/workflows/1470?version=2 |
microbiome/taxonomic-profiling |
True |
False |
|
kraken_taxonomy_report |
kraken_taxonomy_report |
tabular, txt |
Kraken taxonomy report |
2016-06-01 |
https://github.com/blankenberg/Kraken-Taxonomy-Report |
0.0.3 |
biopython |
1.70 |
To update |
Metagenomics |
Visualisation, Classification |
Visualisation, Classification |
Metagenomics, Taxonomy |
Metagenomics, Taxonomy |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report |
Kraken-Taxonomy-Report |
Kraken-Taxonomy-Report |
view report of classification for multiple samples |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1148 |
1155 |
5719 |
5735 |
1291 |
1717 |
5613 |
7684 |
148 |
148 |
587 |
587 |
10 |
10 |
25 |
25 |
14031 |
11944 |
3030 |
2597 |
https://usegalaxy.eu/published/workflow?id=2e5e6291cd112225, https://usegalaxy.eu/published/workflow?id=b659069edd9b1d4e |
|
True |
False |
|
krakentools |
krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa |
txt, tabular, fasta.gz |
KrakenTools is a suite of scripts to be used alongside the Kraken |
2023-01-13 |
https://github.com/jenniferlu717/KrakenTools |
1.2.1 |
krakentools |
1.2.1 |
Up-to-date |
Metagenomics |
Visualisation, Aggregation |
Visualisation, Aggregation |
Taxonomy, Metagenomics |
Taxonomy, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools |
krakentools |
KrakenTools |
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files |
|
6 |
6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
6 |
1 |
0 |
2603 |
2603 |
161915 |
161915 |
1861 |
1861 |
40010 |
40010 |
488 |
488 |
18602 |
18602 |
64 |
64 |
5824 |
5824 |
226351 |
226351 |
5016 |
5016 |
https://usegalaxy.eu/published/workflow?id=0590554db9794d13, https://usegalaxy.eu/published/workflow?id=10101558b211a782, https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc, https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302, https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=6f878d8b43ef1521, https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c, https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=b37800d990cceb83, https://usegalaxy.eu/published/workflow?id=b4809f13c8f0c0be, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=ed2df13cfbc86b99, https://usegalaxy.eu/published/workflow?id=f97e6fe1fcbc53a7, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=131636a795bac485, https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b, https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2, https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, https://usegalaxy.org.au/published/workflow?id=d9ba165e6ae55417, https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56, https://usegalaxy.org/published/workflow?id=3011f5dbf884c9bc, https://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38b, https://usegalaxy.org/published/workflow?id=574e42683dc3961b, https://usegalaxy.org/published/workflow?id=60f0d0d5d6e93941, https://usegalaxy.org/published/workflow?id=7321c6ad5425d347, https://usegalaxy.org/published/workflow?id=8f5904693b5f74f4, https://usegalaxy.org/published/workflow?id=9ba6da7dae465d3e, https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a, https://usegalaxy.org/published/workflow?id=d5436cee11a34de9, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1059?version=1, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/1431?version=1, https://workflowhub.eu/workflows/1439?version=1, https://workflowhub.eu/workflows/1470?version=2, https://workflowhub.eu/workflows/1483?version=1, https://workflowhub.eu/workflows/1492?version=2, https://workflowhub.eu/workflows/2024?version=2 |
microbiome/beer-data-analysis, microbiome/diversity, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling |
True |
False |
|
krocus |
krocus |
tabular, fastq |
Predict MLST directly from uncorrected long reads |
2019-09-03 |
https://github.com/quadram-institute-bioscience/krocus |
1.0.1 |
krocus |
1.0.3 |
To update |
Sequence Analysis |
Multilocus sequence typing, k-mer counting |
Multilocus sequence typing, k-mer counting |
Public health and epidemiology |
Public health and epidemiology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus |
krocus |
krocus |
Predict MLST directly from uncorrected long reads |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
lca_wrapper |
lca1 |
taxonomy |
Find lowest diagnostic rank |
2014-01-27 |
https://bitbucket.org/natefoo/taxonomy |
1.0.1 |
taxonomy |
0.10.2 |
To update |
Metagenomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
3 |
20 |
11 |
137 |
14 |
1112 |
112 |
6136 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6273 |
123 |
1132 |
17 |
https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c |
|
True |
False |
|
legsta |
legsta |
tabular |
Performs in silico Legionella pneumophila sequence based typing. |
2022-02-21 |
https://github.com/tseemann/legsta |
0.5.1 |
legsta |
0.5.2 |
To update |
Sequence Analysis |
Sequence analysis |
Sequence analysis |
Public health and epidemiology |
Public health and epidemiology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta |
legsta |
legsta |
Performs in silico Legionella pneumophila sequence based typing |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
13 |
13 |
134 |
134 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
134 |
134 |
13 |
13 |
|
|
True |
False |
|
lighter |
lighter |
|
Lighter is a kmer-based error correction method for whole genome sequencing data |
2016-06-04 |
https://github.com/mourisl/Lighter |
1.0 |
lighter |
1.1.3 |
To update |
Sequence Analysis, Fasta Manipulation |
k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection |
k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection |
Sequencing, Whole genome sequencing, DNA, Genomics |
Whole genome sequencing, DNA, Genomics |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/lighter |
https://github.com/bgruening/galaxytools/tree/master/tools/lighter |
lighter |
Lighter |
Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
31 |
37 |
106 |
196 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
196 |
106 |
37 |
31 |
|
|
True |
False |
|
limma_voom |
limma_voom |
html, tabular, txt |
Perform RNA-Seq differential expression analysis using limma voom pipeline |
2017-05-24 |
http://bioconductor.org/packages/release/bioc/html/limma.html |
3.58.1 |
bioconductor-limma |
3.66.0 |
To update |
Transcriptomics, RNA, Statistics |
RNA-Seq analysis |
RNA-Seq analysis |
Molecular biology, Genetics |
Molecular biology, Genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom |
limma |
limma |
Data analysis, linear models and differential expression for microarray data. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
2902 |
3166 |
27013 |
30001 |
5247 |
6265 |
50381 |
59995 |
921 |
1003 |
10130 |
11326 |
26 |
26 |
329 |
329 |
101651 |
87853 |
10460 |
9096 |
https://usegalaxy.eu/published/workflow?id=09c77b6fc5add851, https://usegalaxy.eu/published/workflow?id=14226641bba951f3, https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=1c1083b159e5bfb2, https://usegalaxy.eu/published/workflow?id=1d2e17a4f71f2455, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=227d97974573aaf2, https://usegalaxy.eu/published/workflow?id=263eed267aa3e76b, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2ecf737b53f77cf8, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=2f7c04ad219a9d2d, https://usegalaxy.eu/published/workflow?id=3386856a60b35897, https://usegalaxy.eu/published/workflow?id=47f2c44d79896f08, https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6d47a24218d08930, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=7036a6cf67d53bc7, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=8ab363878cd34ef0, https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37, https://usegalaxy.eu/published/workflow?id=8cd275b30524b383, https://usegalaxy.eu/published/workflow?id=8eeb84d58218e44f, https://usegalaxy.eu/published/workflow?id=8f095e5b9594b098, https://usegalaxy.eu/published/workflow?id=9a83043d5e847318, https://usegalaxy.eu/published/workflow?id=ad3be77eb2e8c10e, https://usegalaxy.eu/published/workflow?id=bb4ecac751a94c79, https://usegalaxy.eu/published/workflow?id=c8deb8952abce1ec, https://usegalaxy.eu/published/workflow?id=d6eb0562d0036940, https://usegalaxy.eu/published/workflow?id=dd8b55e7768843b1, https://usegalaxy.eu/published/workflow?id=e8a17b0576df4007, https://usegalaxy.eu/published/workflow?id=f28459c5b16549b7, https://usegalaxy.eu/published/workflow?id=f9ddc4dd9140b293, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.eu/published/workflow?id=fe6c64676be56ee9, https://usegalaxy.org.au/published/workflow?id=bdb498b1f0e8944f, https://usegalaxy.org/published/workflow?id=07fdeadce7a6d5cb, https://usegalaxy.org/published/workflow?id=092be3cf6e40282c, https://usegalaxy.org/published/workflow?id=0a009cf9e88171f1, https://usegalaxy.org/published/workflow?id=0c052e50594f6d2d, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=204d0da8a023d7da, https://usegalaxy.org/published/workflow?id=228ae7f537a60226, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=427fce51fd9508eb, https://usegalaxy.org/published/workflow?id=43c39bc86399188f, https://usegalaxy.org/published/workflow?id=5203bc68df3cf819, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=93650de42fb8c015, https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=b3823d276917baf0, https://usegalaxy.org/published/workflow?id=cd56ed91856fcc6f, https://usegalaxy.org/published/workflow?id=d5514e327878b531, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=dec0cf06fa059e65, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1703?version=1, https://workflowhub.eu/workflows/689?version=1 |
transcriptomics/minerva-pathways, transcriptomics/rna-seq-counts-to-genes |
True |
False |
|
lineagespot |
lineagespot |
tabular |
Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) |
2023-07-04 |
https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html |
1.6.0 |
r-base |
|
To update |
Metagenomics, Sequence Analysis |
Variant calling |
Variant calling |
Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation |
Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot |
lineagespot |
lineagespot |
Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
4 |
4 |
39 |
39 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
39 |
39 |
4 |
4 |
|
|
True |
False |
|
logol |
logol_wrapper |
txt, zip |
Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence |
2018-06-06 |
http://logol.genouest.org/web/app.php/logol |
1.7.8 |
logol |
1.7.8 |
Up-to-date |
Sequence Analysis |
|
|
|
|
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/logol |
https://github.com/genouest/galaxy-tools/tree/master/tools/logol |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
longdust |
longdust |
bed |
Detect low-complexity regions in long DNA sequences using k-mer statistics. |
2025-10-01 |
https://github.com/lh3/longdust |
1.4 |
longdust |
1.4 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust |
|
|
|
|
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
longorf |
longORF |
fasta, tabular |
obtain longest ORF in six-frame translations |
2018-06-01 |
|
0.3.0 |
|
|
To update |
Sequence Analysis |
|
|
|
|
mbernt |
https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
lorikeet_spoligotype |
lorikeet_spoligotype |
txt |
Tools for M. tuberculosis DNA fingerprinting (spoligotyping) |
2018-05-07 |
https://github.com/AbeelLab/lorikeet |
20 |
lorikeet |
20 |
Up-to-date |
Sequence Analysis |
Sequence analysis, Genotyping |
Sequence analysis, Genotyping |
Genotype and phenotype |
Genotype and phenotype |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet |
lorikeet |
lorikeet |
Tools for M. tuberculosis DNA fingerprinting (spoligotyping) |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
18 |
18 |
930 |
930 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
930 |
930 |
18 |
18 |
|
|
True |
False |
|
lotus2 |
lotus2 |
zip, tabular, fasta, newick, txt |
LotuS2 OTU processing pipeline |
2021-05-13 |
https://lotus2.earlham.ac.uk/ |
2.32 |
lotus2 |
2.34.1 |
To update |
Metagenomics |
Sequence feature detection, DNA barcoding |
Sequence feature detection, DNA barcoding |
Metagenomics, Taxonomy, Microbial ecology |
Metagenomics, Taxonomy, Microbial ecology |
earlhaminst |
https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/lotus2 |
https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/lotus2 |
lotus2 |
lotus2 |
LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
249 |
249 |
1979 |
1979 |
0 |
0 |
0 |
0 |
22 |
22 |
417 |
417 |
2 |
2 |
5 |
5 |
2401 |
2401 |
273 |
273 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://workflowhub.eu/workflows/1460?version=1 |
microbiome/lotus2-identifying-fungi, microbiome/mgnify-amplicon |
True |
False |
|
m6anet |
m6anet |
tabular |
m6anet to detect m6A RNA modifications from nanopore data |
2023-10-25 |
https://m6anet.readthedocs.io/en/latest |
2.1.0 |
m6anet |
2.1.0 |
Up-to-date |
Sequence Analysis |
Quantification, Imputation, Gene expression profiling |
Quantification, Imputation, Gene expression profiling |
RNA-Seq, Transcriptomics, RNA, Machine learning |
RNA-Seq, Transcriptomics, RNA, Machine learning |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet |
m6Anet |
m6Anet |
Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
12 |
12 |
47 |
47 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
47 |
47 |
12 |
12 |
|
|
True |
False |
|
maaslin2 |
maaslin2 |
zip, tabular, rdata, pdf |
MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. |
2021-11-05 |
http://huttenhower.sph.harvard.edu/maaslin |
1.18.0 |
bioconductor-maaslin2 |
1.18.0 |
Up-to-date |
Metagenomics |
Filtering, Statistical calculation, Standardisation and normalisation, Visualisation |
Filtering, Standardisation and normalisation, Visualisation |
Metagenomics, Statistics and probability |
Metagenomics, Statistics and probability |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 |
maaslin2 |
MaAsLin2 |
MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
100 |
100 |
3676 |
3676 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
4 |
4 |
3680 |
3680 |
102 |
102 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4ddf2ec5c460d622, https://usegalaxy.eu/published/workflow?id=e1296dbcf34499b0, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 |
|
True |
False |
|
maaslin3 |
maaslin3 |
tabular, png, pdf |
MaAsLin 3 is the next generation of MaAsLin. This comprehensive R package efficiently determines multivariable associations between clinical metadata and microbial meta-omics features. |
2025-11-05 |
https://github.com/biobakery/maaslin3 |
0.99.16 |
maaslin3 |
0.99.16 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin3 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin3 |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
mafft |
rbc_mafft_add, rbc_mafft |
fasta, tabular, txt |
Multiple alignment program for amino acid or nucleotide sequences |
2015-06-16 |
https://mafft.cbrc.jp/alignment/software/ |
7.526 |
mafft |
7.525 |
To update |
RNA |
Multiple sequence alignment |
Multiple sequence alignment |
Sequence analysis |
Sequence analysis |
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/mafft |
https://github.com/bgruening/galaxytools/tree/master/tools/mafft |
MAFFT |
MAFFT |
MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
2 |
2 |
2 |
0 |
2844 |
3060 |
164403 |
217226 |
4659 |
6641 |
99571 |
145229 |
1279 |
1462 |
23332 |
25716 |
158 |
160 |
5367 |
5382 |
393553 |
292673 |
11323 |
8940 |
https://usegalaxy.eu/published/workflow?id=402b14906a03b2ef, https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60, https://usegalaxy.eu/published/workflow?id=941400d10c346b2c, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=b1a799497c366eef, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.eu/published/workflow?id=d102a20c31d4673c, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.eu/published/workflow?id=e97b938ca4723827, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=b3974acb70608e38, https://usegalaxy.fr/published/workflow?id=c7be6e229a045fad, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://usegalaxy.fr/published/workflow?id=e134e9637adfc5b6, https://usegalaxy.org.au/published/workflow?id=3242ec69dec6e13f, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a, https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3, https://usegalaxy.org.au/published/workflow?id=d62b6717202f42c9, https://usegalaxy.org.au/published/workflow?id=f21446cc44da50ce, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=8d8e8927d63803ef, https://usegalaxy.org/published/workflow?id=956987e628530c79, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://usegalaxy.org/published/workflow?id=be54e57345ce7ca5, https://usegalaxy.org/published/workflow?id=f737593a1db217c8, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1559?version=1, https://workflowhub.eu/workflows/1627?version=1, https://workflowhub.eu/workflows/1650?version=1, https://workflowhub.eu/workflows/1839?version=1 |
evolution/abc_intro_phylo, genome-annotation/gene-centric, sequence-analysis/tapscan-streptophyte-algae, sequence-analysis/viral_primer_design, variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon |
True |
False |
|
make_nr |
make_nr |
fasta |
Make a FASTA file non-redundant |
2018-11-06 |
https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr |
0.0.3 |
biopython |
1.70 |
To update |
Fasta Manipulation, Sequence Analysis |
Sequence alignment, Genome annotation |
Sequence alignment, Genome annotation |
Molecular biology, Sequence analysis |
Molecular biology, Sequence analysis |
peterjc |
https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr |
https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr |
make_nr |
make_nr |
Make a FASTA file non-redundant, with a Galaxy wrapperThis tool is copyright 2018 by Peter Cock, The James Hutton Institute, UK. All rights reserved.This tool is a short Python script intended to be run prior to calling the NCBI BLAST+ command line tool makeblastdb or in other settings where you want to collapse duplicated sequences in a FASTA file to a single representative. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
maker |
maker, maker_map_ids |
gff3, gff, tabular |
MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. |
2017-10-04 |
http://www.yandell-lab.org/software/maker.html |
2.31.11 |
maker |
3.01.04 |
To update |
Sequence Analysis |
Genome annotation |
Genome annotation |
Genomics, DNA, Sequence analysis |
Genomics, DNA, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker |
maker |
MAKER |
Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
0 |
1323 |
1455 |
7332 |
8835 |
1701 |
1808 |
9536 |
10359 |
904 |
904 |
4968 |
4989 |
33 |
33 |
211 |
211 |
24394 |
22047 |
4200 |
3961 |
https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=65b4051e722228b8, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43, https://workflowhub.eu/workflows/1323?version=1, https://workflowhub.eu/workflows/1504?version=1, https://workflowhub.eu/workflows/1549?version=1 |
genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short |
True |
False |
|
mapseq |
mapseq |
tabular |
fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. |
2023-08-02 |
https://github.com/jfmrod/MAPseq |
2.1.1b |
perl |
|
To update |
Metagenomics |
k-mer counting |
k-mer counting |
Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs |
Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq |
mapseq |
MAPseq |
Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . |
|
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
64 |
64 |
9612 |
9612 |
24 |
24 |
434 |
434 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10046 |
10046 |
88 |
88 |
https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=fb806b88850f3427, https://usegalaxy.org/published/workflow?id=45f959d5bf505b15, https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1 |
microbiome/mgnify-amplicon |
True |
False |
|
marine_omics |
sanntis_marine |
gff3, genbank |
The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data |
2024-07-26 |
https://github.com/Finn-Lab/SanntiS |
0.9.3.5 |
sanntis |
0.9.4.1 |
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
22 |
22 |
198 |
198 |
0 |
0 |
0 |
0 |
5 |
5 |
112 |
112 |
0 |
0 |
0 |
0 |
310 |
310 |
27 |
27 |
https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://workflowhub.eu/workflows/1663?version=1 |
ecology/marine_omics_bgc |
True |
False |
|
mash |
mash_dist, mash_paste, mash_screen, mash_sketch |
tsv, msh, tabular |
Fast genome and metagenome distance estimation using MinHash |
2018-12-07 |
https://github.com/marbl/Mash |
2.3 |
mash |
2.3 |
Up-to-date |
Metagenomics |
Sequence distance matrix generation |
Sequence distance matrix generation |
Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation |
Metagenomics, Statistics and probability, Sequence analysis, DNA mutation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash |
mash |
Mash |
Fast genome and metagenome distance estimation using MinHash. |
|
4 |
2 |
4 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
4 |
2 |
0 |
49 |
57 |
10768 |
10867 |
18 |
18 |
922 |
922 |
18 |
18 |
3187 |
3187 |
3 |
3 |
29 |
29 |
15005 |
14906 |
96 |
88 |
|
|
True |
False |
|
maxbin2 |
maxbin2 |
fasta, tabular, txt, pdf |
clusters metagenomic contigs into bins |
2019-10-24 |
https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html |
|
maxbin2 |
2.2.7 |
To update |
Metagenomics |
Sequence assembly |
Sequence assembly |
Metagenomics, Sequence assembly, Microbiology |
Metagenomics, Sequence assembly, Microbiology |
mbernt |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 |
maxbin |
MaxBin |
Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
408 |
433 |
5244 |
5537 |
634 |
675 |
2694 |
2993 |
106 |
108 |
1135 |
1198 |
6 |
6 |
648 |
648 |
10376 |
9721 |
1222 |
1154 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=972da31ce19c0beb, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1 |
microbiome/metagenomics-binning |
True |
False |
|
maxquant |
maxquant, maxquant_mqpar |
|
wrapper for MaxQuant |
2015-01-24 |
https://www.maxquant.org/ |
2.0.3.0 |
maxquant |
2.0.3.0 |
Up-to-date |
Proteomics |
Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting |
Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering |
Proteomics experiment, Proteomics, Statistics and probability |
Proteomics experiment, Proteomics, Statistics and probability |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant |
maxquant |
MaxQuant |
Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
0 |
1628 |
1682 |
7932 |
8757 |
775 |
775 |
3791 |
3791 |
407 |
416 |
3720 |
3831 |
3 |
3 |
33 |
33 |
16412 |
15476 |
2876 |
2813 |
https://usegalaxy.eu/published/workflow?id=0135ee4b3fa0cbce, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=96d198ed953449fd, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=d789165f4e0c50eb, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://usegalaxy.org.au/published/workflow?id=43a951ec514498f6, https://usegalaxy.org.au/published/workflow?id=781457327e644c7e, https://usegalaxy.org.au/published/workflow?id=b0a79310e0dc3fb4, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=2404d5e5b1817825, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1177?version=1, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1401?version=1, https://workflowhub.eu/workflows/1420?version=1, https://workflowhub.eu/workflows/1421?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1448?version=1, https://workflowhub.eu/workflows/1468?version=1 |
microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-4-quantitation, proteomics/DIA_lib_OSW, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-4-quantitation, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq, proteomics/maxquant-msstats-tmt |
True |
False |
|
mcl |
mcl |
tabular |
The Markov Cluster Algorithm, a cluster algorithm for graphs |
2022-05-12 |
https://micans.org/mcl/man/mcl.html |
22.282 |
mcl |
22.282 |
Up-to-date |
Sequence Analysis |
Clustering, Network analysis, Gene regulatory network analysis |
Clustering, Gene regulatory network analysis |
Molecular interactions, pathways and networks |
Molecular interactions, pathways and networks |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl |
mcl |
MCL |
MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
18 |
18 |
153 |
153 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
153 |
153 |
18 |
18 |
|
|
True |
False |
|
medaka |
medaka_consensus, medaka_consensus_pipeline, medaka_variant |
h5, txt, fasta, bam, bed, vcf, tabular |
Sequence correction provided by ONT Research |
2020-02-23 |
https://github.com/nanoporetech/medaka |
2.1.1 |
medaka |
2.2.0 |
To update |
Sequence Analysis |
Base-calling, Variant calling, Sequence assembly |
Base-calling, Variant calling, Sequence assembly |
Sequence assembly, Machine learning |
Sequence assembly, Machine learning |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka |
medaka |
Medaka |
medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. |
|
3 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
3 |
3 |
3 |
0 |
1728 |
1734 |
155538 |
156220 |
735 |
735 |
76698 |
76698 |
421 |
421 |
11622 |
11622 |
17 |
17 |
2659 |
2659 |
247199 |
246517 |
2907 |
2901 |
https://usegalaxy.eu/published/workflow?id=0f6a7bd5362e4a2b, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2d9d4445a1871230, https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df, https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef, https://usegalaxy.eu/published/workflow?id=429ae28a178cd07c, https://usegalaxy.eu/published/workflow?id=476db04368d5e90c, https://usegalaxy.eu/published/workflow?id=4d97068a725c975c, https://usegalaxy.eu/published/workflow?id=529f30e894beacc2, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=70d3ebf31940bfb3, https://usegalaxy.eu/published/workflow?id=77e5bbd317750915, https://usegalaxy.eu/published/workflow?id=7bdd9ad918edab0b, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=b97532c398b821a2, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=cf8591391a17a914, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.fr/published/workflow?id=61235264d5d2f666, https://usegalaxy.fr/published/workflow?id=727cfdb7c79287d1, https://usegalaxy.fr/published/workflow?id=e3c04a30258421aa, https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060, https://usegalaxy.org.au/published/workflow?id=0c6f7bfc826433c4, https://usegalaxy.org.au/published/workflow?id=47ce6a2d30887637, https://usegalaxy.org.au/published/workflow?id=48a60965b6b3ff54, https://usegalaxy.org.au/published/workflow?id=4bc8ac41ecff7daf, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=705658f68ae73930, https://usegalaxy.org.au/published/workflow?id=888f8377eb6eabf2, https://usegalaxy.org.au/published/workflow?id=932bad88f8dc8d33, https://usegalaxy.org.au/published/workflow?id=ba7a9d4c857d26b7, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5, https://usegalaxy.org/published/workflow?id=4357180d40560019, https://usegalaxy.org/published/workflow?id=48dafc35989f13b1, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=88d0b64011c3148c, https://usegalaxy.org/published/workflow?id=953d9cbe05e632a8, https://usegalaxy.org/published/workflow?id=9adf8691809326e5, https://usegalaxy.org/published/workflow?id=c12e6b7896f8e114, https://usegalaxy.org/published/workflow?id=c7b2d2ccc4b0dec5, https://usegalaxy.org/published/workflow?id=cce88bc57b180d09, https://usegalaxy.org/published/workflow?id=d3428dd172a78102, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/111?version=5, https://workflowhub.eu/workflows/1495?version=1, https://workflowhub.eu/workflows/1578?version=1, https://workflowhub.eu/workflows/226?version=1 |
assembly/largegenome, microbiome/pathogen-detection-from-nanopore-foodborne-data |
True |
False |
|
megahit |
megahit |
fasta, txt |
An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. |
2017-09-22 |
https://github.com/voutcn/megahit |
1.2.9 |
megahit |
1.2.9 |
Up-to-date |
Sequence Analysis, Assembly, Metagenomics |
Genome assembly |
Genome assembly |
Metagenomics, Sequencing, Ecology, Sequence assembly |
Metagenomics, Sequencing, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit |
megahit |
MEGAHIT |
Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
2052 |
2197 |
22340 |
24371 |
2823 |
2929 |
23973 |
24874 |
615 |
632 |
9338 |
9643 |
54 |
54 |
1387 |
1387 |
60275 |
57038 |
5812 |
5544 |
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assembly/metagenomics-assembly, microbiome/metagenomics-assembly |
True |
False |
|
megahit_contig2fastg |
megahit_contig2fastg |
fastg |
A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) |
2018-11-09 |
https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp |
1.1.3 |
megahit |
1.2.9 |
To update |
Sequence Analysis, Assembly, Metagenomics |
Genome assembly |
Genome assembly |
Metagenomics, Sequencing, Ecology, Sequence assembly |
Metagenomics, Sequencing, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg |
megahit |
MEGAHIT |
Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
200 |
212 |
763 |
862 |
113 |
113 |
338 |
338 |
33 |
33 |
150 |
150 |
6 |
6 |
80 |
80 |
1430 |
1331 |
364 |
352 |
https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1634?version=1 |
assembly/metagenomics-assembly, microbiome/metagenomics-assembly |
True |
False |
|
megan |
megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma |
txt, rma6, daa |
MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). |
2021-11-24 |
https://github.com/husonlab/megan-ce |
6.21.7 |
megan |
6.25.10 |
To update |
Sequence Analysis |
Sequence analysis, Taxonomic classification |
Sequence analysis, Taxonomic classification |
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan |
megan |
MEGAN |
Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. |
|
0 |
1 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
0 |
0 |
250 |
250 |
5164 |
5164 |
0 |
0 |
0 |
0 |
5 |
5 |
72 |
72 |
3 |
3 |
4 |
4 |
5240 |
5240 |
258 |
258 |
|
|
True |
False |
|
meningotype |
meningotype |
tabular |
Assign sequence type to N. meningitidis genome assemblies |
2023-06-06 |
https://github.com/MDU-PHL/meningotype |
0.8.5 |
meningotype |
0.8.5 |
Up-to-date |
Sequence Analysis |
Genotyping, Multilocus sequence typing |
Multilocus sequence typing |
Microbiology, Genotype and phenotype |
Microbiology, Genotype and phenotype |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype |
meningotype |
meningotype |
In silico typing of Neisseria meningitidis contigs. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
merqury |
merqury, merquryplot |
txt |
Merqury is a tool for evaluating genomes assemblies based of k-mer operations. |
2021-04-18 |
https://github.com/marbl/merqury |
1.3 |
merqury |
1.3 |
Up-to-date |
Assembly |
Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly |
Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly |
Sequence assembly, Whole genome sequencing, Plant biology |
Sequence assembly, Whole genome sequencing, Plant biology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury |
merqury |
Merqury |
Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
0 |
661 |
661 |
4657 |
4657 |
264 |
264 |
1645 |
1645 |
243 |
243 |
1945 |
1945 |
77 |
77 |
440 |
440 |
8687 |
8687 |
1245 |
1245 |
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https://workflowhub.eu/workflows/794?version=2 |
assembly/ERGA-post-assembly-QC, assembly/assembly-quality-control, assembly/vgp_genome_assembly |
True |
False |
|
meryl |
meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode |
meryldb, tabular |
Meryl a k-mer counter. |
2021-04-05 |
https://github.com/marbl/meryl |
1.4.1 |
merqury |
1.3 |
To update |
Assembly |
k-mer counting |
k-mer counting |
Whole genome sequencing, Genomics, Sequence analysis, Sequencing |
Whole genome sequencing, Genomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl |
meryl |
Meryl |
Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. |
|
7 |
0 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
55 |
55 |
1850 |
1850 |
77 |
77 |
1478 |
1478 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3328 |
3328 |
132 |
132 |
https://usegalaxy.eu/published/workflow?id=0ccb3838765a8b84, https://usegalaxy.eu/published/workflow?id=10bde4e7f8dbd0c4, https://usegalaxy.eu/published/workflow?id=41c48e4632684f76, https://usegalaxy.eu/published/workflow?id=59f35cb60b3d989d, https://usegalaxy.org/published/workflow?id=4b919e575a16d062, https://usegalaxy.org/published/workflow?id=5503f7835226bc04, https://usegalaxy.org/published/workflow?id=6988c29ae84d2788, https://usegalaxy.org/published/workflow?id=83898f7cbfb7f88e, https://usegalaxy.org/published/workflow?id=9f1aabc6f5d18d13, https://usegalaxy.org/published/workflow?id=af1f4dba9aaa0b52, https://usegalaxy.org/published/workflow?id=b4f9d9aafe87af82, https://usegalaxy.org/published/workflow?id=beefb67de2b0728c, https://workflowhub.eu/workflows/631?version=6, https://workflowhub.eu/workflows/632?version=13 |
|
True |
False |
|
metabat2 |
metabat2_jgi_summarize_bam_contig_depths, metabat2 |
tabular, fasta, txt |
MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. |
2022-01-28 |
https://bitbucket.org/berkeleylab/metabat/src/master/ |
2.17 |
metabat2 |
2.18 |
To update |
Metagenomics |
Read binning, Sequence assembly, Genome annotation |
Read binning, Sequence assembly, Genome annotation |
Metagenomics, Sequence assembly, Metagenomic sequencing |
Metagenomics, Sequence assembly, Metagenomic sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 |
MetaBAT_2 |
MetaBAT 2 |
an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
2 |
2 |
0 |
0 |
670 |
670 |
14194 |
14194 |
375 |
375 |
2591 |
2591 |
167 |
167 |
1738 |
1738 |
18 |
18 |
1359 |
1359 |
19882 |
19882 |
1230 |
1230 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1 |
microbiome/metagenomics-binning |
True |
False |
|
metabuli |
metabuli_classify |
tabular, html, txt |
Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences |
2024-06-04 |
https://github.com/steineggerlab/Metabuli |
1.0.5 |
metabuli |
1.1.0 |
To update |
Sequence Analysis, Metagenomics |
Taxonomic classification |
Taxonomic classification |
Taxonomy |
Taxonomy |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli |
metabuli |
metabuli |
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
metaeuk |
metaeuk_easy_predict |
fasta, gff |
MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. |
2020-08-04 |
https://github.com/soedinglab/metaeuk |
7.bba0d80 |
metaeuk |
6.a5d39d9 |
To update |
Sequence Analysis, Genome annotation |
Homology-based gene prediction |
Homology-based gene prediction |
Metagenomics, Gene and protein families |
Metagenomics, Gene and protein families |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk |
MetaEuk |
MetaEuk |
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
57 |
58 |
507 |
509 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
509 |
507 |
58 |
57 |
https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 |
|
True |
False |
|
metagene_annotator |
metagene_annotator |
txt, tabular, bed |
MetaGeneAnnotator gene-finding program for prokaryote and phage |
2018-03-21 |
http://metagene.nig.ac.jp/ |
1.0 |
metagene_annotator |
1.0 |
Up-to-date |
Sequence Analysis |
Sequence annotation |
Sequence annotation |
Genomics, Model organisms, Data submission, annotation and curation |
Genomics, Model organisms, Data submission, annotation and curation |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator |
metageneannotator |
MetaGeneAnnotator |
Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
439 |
457 |
20971 |
21069 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21069 |
20971 |
457 |
439 |
https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=799b924edd3c401b, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178 |
|
True |
False |
|
metagenomeseq_normalization |
metagenomeseq_normalizaton |
tabular, txt |
metagenomeSeq Normalization |
2017-03-27 |
https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html |
1.16.0-0.0.1 |
bioconductor-metagenomeseq |
1.52.0 |
To update |
Metagenomics |
Sequence visualisation, Statistical calculation |
Sequence visualisation, Statistical calculation |
Metagenomics, Sequencing |
Metagenomics, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq |
metagenomeseq |
metagenomeSeq |
Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. |
|
1 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
15 |
23 |
521 |
763 |
28 |
56 |
261 |
530 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1293 |
782 |
79 |
43 |
|
|
True |
False |
|
metamdbg |
metamdbg_asm, metamdbg_gfa |
fasta.gz, tar.gz, txt, gfa1 |
MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads. |
2026-01-21 |
https://github.com/GaetanBenoitDev/metaMDBG |
1.3 |
metamdbg |
1.3 |
Up-to-date |
Assembly, Metagenomics |
Genome assembly |
Genome assembly |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metamdbg |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metamdbg |
metamdbg |
metaMDBG |
MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads (e.g. PacBio HiFi, Nanopore r10.4). It is based on the minimizer de-Brujin graph (MDBG), which have been reimplemetend specifically for metagenomics assembly. MetaMDBG combines an efficient multi-k approach in minimizer-space for dealing with uneven species coverages, and a novel abundance-based filtering method for simplifying strain complexity. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
metanovo |
metanovo |
fasta, csv |
Produce targeted databases for mass spectrometry analysis. |
2022-03-29 |
https://github.com/uct-cbio/proteomics-pipelines |
1.9.4 |
metanovo |
1.9.4 |
Up-to-date |
Proteomics |
Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis |
Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis |
Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules |
Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo |
metanovo |
MetaNovo |
An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. |
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
40 |
40 |
5000 |
5000 |
5 |
5 |
34 |
34 |
4 |
4 |
92 |
92 |
0 |
0 |
0 |
0 |
5126 |
5126 |
49 |
49 |
https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18, https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=d7c7a4d6c8072167, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.org.au/published/workflow?id=351f3fab960c013b, https://usegalaxy.org/published/workflow?id=2be8ecd5922d23d1, https://workflowhub.eu/workflows/1216?version=1, https://workflowhub.eu/workflows/1461?version=1, https://workflowhub.eu/workflows/1474?version=1 |
microbiome/clinical-mp-1-database-generation, proteomics/clinical-mp-1-database-generation |
True |
False |
|
metaphlan |
customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan |
fasta, json, tabular, sam, biom1, fastqsanger |
MetaPhlAn for Metagenomic Phylogenetic Analysis |
2021-03-11 |
https://github.com/biobakery/MetaPhlAn |
4.2.4 |
metaphlan |
4.2.4 |
Up-to-date |
Metagenomics |
Taxonomic classification, Taxonomic classification |
Taxonomic classification, Taxonomic classification |
Metagenomics, Phylogenomics |
Metagenomics, Phylogenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan |
metaphlan |
MetaPhlAn |
Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. |
|
1 |
2 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
4 |
4 |
0 |
1552 |
1552 |
30934 |
31014 |
1122 |
1122 |
20021 |
20021 |
314 |
314 |
6347 |
6347 |
28 |
28 |
211 |
211 |
57593 |
57513 |
3016 |
3016 |
https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.org.au/published/workflow?id=6b7e565258a9da2a, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2, https://workflowhub.eu/workflows/1470?version=2, https://workflowhub.eu/workflows/624?version=1 |
microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/taxonomic-profiling |
True |
False |
|
metaquantome |
metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz |
tar, tabular, html |
quantitative analysis of microbiome taxonomy and function |
2018-11-27 |
https://github.com/galaxyproteomics/metaquantome/ |
2.0.2 |
metaquantome |
2.0.2 |
Up-to-date |
Proteomics |
Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference |
Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference |
Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics |
Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome |
metaQuantome |
metaQuantome |
metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. |
|
0 |
6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
6 |
0 |
80 |
89 |
2277 |
3166 |
0 |
0 |
0 |
0 |
27 |
27 |
2323 |
2323 |
0 |
0 |
0 |
0 |
5489 |
4600 |
116 |
107 |
https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba, https://usegalaxy.eu/published/workflow?id=695f7defb516d80d, https://usegalaxy.eu/published/workflow?id=ce7f7c6eef526d67, https://usegalaxy.eu/published/workflow?id=dc438d4ae1866df8, https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9, https://usegalaxy.org.au/published/workflow?id=cada735fa0716570, https://usegalaxy.org.au/published/workflow?id=f8183bba3a1d150d, https://workflowhub.eu/workflows/1453?version=1, https://workflowhub.eu/workflows/1459?version=1 |
proteomics/metaquantome-function, proteomics/metaquantome-taxonomy |
True |
False |
|
metasbt |
metasbt_index, metasbt_profile |
tabular, tar |
Microbial genomes characterization with Sequence Bloom Trees |
2025-08-22 |
https://github.com/cumbof/MetaSBT |
0.1.5 |
sed |
|
To update |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt |
|
|
|
|
2 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
metawrapmg_binning |
metawrapmg_binning, metawrapmg_bin_refinement |
|
A flexible pipeline for genome-resolved metagenomic data analysis |
2024-04-11 |
https://github.com/bxlab/metaWRAP |
1.3.0 |
metawrap-mg |
1.3.0 |
Up-to-date |
Metagenomics |
Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing |
Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing |
Whole genome sequencing, Metagenomic sequencing, Metagenomics |
Whole genome sequencing, Metagenomic sequencing, Metagenomics |
galaxy-australia |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg |
metawrap |
MetaWRAP |
MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
100 |
100 |
1596 |
1596 |
0 |
0 |
0 |
0 |
67 |
67 |
587 |
587 |
0 |
0 |
0 |
0 |
2183 |
2183 |
167 |
167 |
|
|
True |
False |
|
mg_toolkit |
mg_toolkit_bulk_download, mg_toolkit_original_metadata |
tsv |
Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. |
2024-07-12 |
https://github.com/EBI-Metagenomics/emg-toolkit |
0.10.4 |
mg-toolkit |
0.10.4 |
Up-to-date |
Metagenomics |
Data retrieval |
Data retrieval |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit |
mg-toolkit |
mg-toolkit |
Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
21 |
21 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21 |
21 |
10 |
10 |
|
|
True |
False |
|
mgnify_seqprep |
mgnify_seqprep |
fastq.gz |
A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. |
2024-05-14 |
https://github.com/jstjohn/SeqPrep |
1.2 |
|
|
To update |
Fastq Manipulation, Sequence Analysis |
Nucleic acid design |
Nucleic acid design |
Genomics, Sequence assembly, Sequencing, Probes and primers |
Genomics, Sequence assembly, Sequencing, Probes and primers |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep |
https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep |
seqprep |
SeqPrep |
Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. |
|
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
6 |
6 |
1348 |
1348 |
109 |
109 |
444 |
444 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1792 |
1792 |
115 |
115 |
https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1854?version=1 |
microbiome/mgnify-amplicon |
True |
False |
|
micro_decon |
micro_decon |
csv |
An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing |
2025-08-05 |
https://github.com/donaldtmcknight/microdecon |
1.0.2 |
|
|
To update |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
minia |
minia |
fasta |
Short-read assembler based on a de Bruijn graph |
2020-04-08 |
https://gatb.inria.fr/software/minia/ |
3.2.6 |
minia |
3.2.6 |
Up-to-date |
Assembly |
Genome assembly |
Genome assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia |
minia |
Minia |
Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
272 |
287 |
6758 |
7224 |
0 |
0 |
0 |
0 |
77 |
77 |
357 |
357 |
0 |
0 |
0 |
0 |
7581 |
7115 |
364 |
349 |
https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40 |
|
True |
False |
|
miniasm |
miniasm |
tabular |
Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) |
2019-06-18 |
https://github.com/lh3/miniasm |
0.3_r179 |
miniasm |
0.3 |
To update |
Assembly |
De-novo assembly |
De-novo assembly |
Genomics, Sequence assembly |
Genomics, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm |
miniasm |
miniasm |
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
571 |
687 |
11506 |
14702 |
474 |
538 |
9124 |
10016 |
88 |
96 |
1235 |
1277 |
16 |
16 |
166 |
166 |
26161 |
22031 |
1337 |
1149 |
https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 |
microbiome/plasmid-metagenomics-nanopore |
True |
False |
|
minipolish |
minipolish |
gfa1 |
Polishing miniasm assemblies |
2022-10-19 |
https://github.com/rrwick/Minipolish |
0.2.0 |
minipolish |
0.2.0 |
Up-to-date |
Sequence Analysis |
Localised reassembly, Read depth analysis |
Localised reassembly, Read depth analysis |
Sequence assembly, Sequencing |
Sequence assembly, Sequencing |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/minipolish |
https://github.com/bgruening/galaxytools/tree/master/tools/minipolish |
minipolish |
minipolish |
A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
43 |
43 |
278 |
278 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
278 |
278 |
43 |
43 |
|
|
True |
False |
|
miniprot |
miniprot, miniprot_index |
gff3, binary |
Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. |
2022-09-19 |
https://github.com/lh3/miniprot |
0.18 |
miniprot |
0.18 |
Up-to-date |
Sequence Analysis |
Sequence alignment, Protein sequence analysis |
Sequence alignment, Protein sequence analysis |
Sequence sites, features and motifs, Sequence analysis |
Sequence sites, features and motifs, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot |
miniprot |
miniprot |
Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. |
|
2 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
100 |
100 |
5038 |
5038 |
42 |
42 |
364 |
364 |
0 |
0 |
0 |
0 |
25 |
25 |
283 |
283 |
5685 |
5685 |
167 |
167 |
https://usegalaxy.eu/published/workflow?id=0c92c3c322c3effe |
|
True |
False |
|
mitos |
mitos, mitos2 |
bed, tabular, gff, txt, fasta, pdf, zip |
de-novo annotation of metazoan mitochondrial genomes |
2020-02-18 |
http://mitos.bioinf.uni-leipzig.de/ |
1.1.7 |
mitos |
2.1.10 |
To update |
Sequence Analysis |
Genome annotation |
Genome annotation |
Zoology, Whole genome sequencing |
Zoology, Whole genome sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos |
mitos |
MITOS |
De novo metazoan mitochondrial genome annotation. |
|
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
0 |
1326 |
1336 |
267673 |
268177 |
772 |
772 |
84561 |
84561 |
151 |
151 |
15492 |
15492 |
6 |
6 |
109 |
109 |
368339 |
367835 |
2265 |
2255 |
https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10, https://usegalaxy.org/published/workflow?id=110ad20060b03e02 |
|
True |
False |
|
mlst |
mlst, mlst_list |
tabular, fasta, txt |
Scan contig files against PubMLST typing schemes |
2016-12-12 |
https://github.com/tseemann/mlst |
2.22.0 |
mlst |
2.32.2 |
To update |
Sequence Analysis |
Multilocus sequence typing |
Multilocus sequence typing |
Immunoproteins and antigens |
Immunoproteins and antigens |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst |
mlst |
MLST |
Multi Locus Sequence Typing from an assembled genome or from a set of reads. |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
0 |
1786 |
1918 |
24365 |
26341 |
1356 |
1420 |
12903 |
13604 |
1137 |
1439 |
12595 |
15564 |
22 |
22 |
99 |
99 |
55608 |
49962 |
4799 |
4301 |
https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=368d1ac0150ea0b6, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=e20172eb0f30d6cd, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be |
microbiome/pathogen-detection-from-nanopore-foodborne-data |
True |
False |
|
mmseqs2 |
mmseqs2_easy_linclust_clustering, mmseqs2_taxonomy_assignment |
fasta, tabular, txt, html |
MMseqs2 is an ultra fast and sensitive sequence search and clustering suite |
2025-03-27 |
https://github.com/soedinglab/MMseqs2 |
17-b804f |
mmseqs2 |
17.b804f |
To update |
Sequence Analysis, Metagenomics |
Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification |
Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification |
Metagenomics, Sequence analysis, Proteins, Nucleic acids, Gene and protein families, Taxonomy |
Metagenomics, Sequence analysis, Nucleic acids, Gene and protein families, Taxonomy |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmseqs2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmseqs2 |
MMseqs2 |
MMseqs2 |
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity. |
|
2 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
42 |
42 |
260 |
260 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
29 |
29 |
289 |
289 |
45 |
45 |
https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://workflowhub.eu/workflows/2024?version=2 |
|
True |
False |
|
mmuphin |
mmuphin |
tabular, pdf |
MMUPHin is an R package implementing meta-analysis methods for microbial community profiles |
2024-11-22 |
https://huttenhower.sph.harvard.edu/mmuphin |
1.16.0 |
bioconductor-mmuphin |
1.16.0 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmuphin |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmuphin |
mmuphin |
mmuphin |
MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
14 |
14 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
14 |
14 |
3 |
3 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 |
|
True |
False |
|
mob_suite |
mob_recon, mob_typer |
tabular, fasta |
MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies |
2018-04-30 |
https://github.com/phac-nml/mob-suite |
3.1.9 |
mob_suite |
3.1.9 |
Up-to-date |
Sequence Analysis |
Clustering, Sequence analysis |
Clustering, Sequence analysis |
Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements, Genomics |
Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements |
nml |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite |
mob_suite |
mob_suite |
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assembliesThe MOB-suite depends on a series of databases which are too large to be hosted in git-hub. They can be downloaded or updated by running mob_init or if running any of the tools for the first time, the databases will download and initialize automatically if you do not specify an alternate database location. |
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
620 |
620 |
162457 |
162457 |
1 |
1 |
42 |
42 |
199 |
199 |
66525 |
66525 |
12 |
12 |
58 |
58 |
229082 |
229082 |
832 |
832 |
https://workflowhub.eu/workflows/407?version=1 |
|
True |
False |
|
mothur |
mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn |
mothur.align.check, mothur.align, mothur.align.report, mothur.accnos, tabular, mothur.shared, mothur.cons.taxonomy, mothur.tax.summary, txt, mothur.freq, mothur.quan, mothur.count_table, mothur.seq.taxonomy, mothur.tre, mothur.lower.dist, mothur.rabund, mothur.sabund, mothur.list, mothur.names, mothur.axes, mothur.groups, mothur.pair.dist, fasta, qual454, fastq, mothur.filter, mothur.design, mothur.otu.corr, mothur.relabund, svg, qual, mothur.sff.flow, sff, xml, mothur.summary |
Mothur wrappers |
2016-06-24 |
https://www.mothur.org |
1.0 |
mothur |
1.48.5 |
To update |
Metagenomics |
DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis |
DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis |
Microbial ecology, Taxonomy, Sequence analysis, Phylogeny |
Microbial ecology, Taxonomy, Sequence analysis, Phylogeny |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur |
mothur |
mothur |
Open-source, platform-independent, community-supported software for describing and comparing microbial communities |
|
129 |
129 |
129 |
129 |
0 |
0 |
0 |
0 |
0 |
0 |
129 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
126 |
129 |
129 |
0 |
2291 |
2805 |
265024 |
361038 |
4027 |
5455 |
423935 |
750968 |
1447 |
1742 |
164152 |
213607 |
147 |
149 |
14583 |
14948 |
1340561 |
867694 |
10151 |
7912 |
https://usegalaxy.eu/published/workflow?id=565c989730f68362, https://usegalaxy.eu/published/workflow?id=6d06bd22f206e176, https://usegalaxy.eu/published/workflow?id=6efd80daabf518bf, https://usegalaxy.eu/published/workflow?id=7783eeebfa264bf5, https://usegalaxy.eu/published/workflow?id=83a0c1ba280785e6, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=b66e1d8171e6dac2, https://usegalaxy.eu/published/workflow?id=b86f24473a282ef9, https://usegalaxy.eu/published/workflow?id=b91a380ceaa0342b, https://usegalaxy.eu/published/workflow?id=c1e26abe61c69688, https://usegalaxy.eu/published/workflow?id=c55388a8fbfd7381, https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19, https://usegalaxy.eu/published/workflow?id=ce21961260fe4351, https://usegalaxy.eu/published/workflow?id=dadca1020f586338, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=177579096e009178, https://usegalaxy.org.au/published/workflow?id=1954437da1e0c4de, https://usegalaxy.org.au/published/workflow?id=2717e90438c7fb8c, https://usegalaxy.org.au/published/workflow?id=2a6324600f159061, https://usegalaxy.org.au/published/workflow?id=57fe85f947217994, https://usegalaxy.org.au/published/workflow?id=5877e2d5eba79f36, https://usegalaxy.org.au/published/workflow?id=58bd08b1530e7cae, https://usegalaxy.org.au/published/workflow?id=670e100ed3c039e2, https://usegalaxy.org.au/published/workflow?id=74bd939615090c2c, https://usegalaxy.org.au/published/workflow?id=7e381c150820e506, https://usegalaxy.org.au/published/workflow?id=832fe9dfc67fd8ed, https://usegalaxy.org.au/published/workflow?id=a52609119b30e64d, https://usegalaxy.org.au/published/workflow?id=fa8d1de86aa944a2, https://usegalaxy.org/published/workflow?id=2d149545a4920326, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=64fa13bb48fcd7df, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=6f090b2c259847d2, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=775335812a6b7a61, https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4, https://usegalaxy.org/published/workflow?id=a383ce2e2bc3c7b9, https://usegalaxy.org/published/workflow?id=b2f3d7e4cd4d0f11, https://usegalaxy.org/published/workflow?id=bc01b8b203ecc754, https://usegalaxy.org/published/workflow?id=cade0c5c11978323, https://usegalaxy.org/published/workflow?id=d653eaefcf6b4697, https://usegalaxy.org/published/workflow?id=d7a11a4dfda3dab4, https://workflowhub.eu/workflows/1400?version=1, https://workflowhub.eu/workflows/1404?version=1, https://workflowhub.eu/workflows/1408?version=1, https://workflowhub.eu/workflows/1412?version=1, https://workflowhub.eu/workflows/1418?version=1, https://workflowhub.eu/workflows/1422?version=1, https://workflowhub.eu/workflows/1428?version=1, https://workflowhub.eu/workflows/1465?version=1, https://workflowhub.eu/workflows/1476?version=1, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1, https://workflowhub.eu/workflows/2038?version=1, https://workflowhub.eu/workflows/648?version=1, https://workflowhub.eu/workflows/649?version=1, https://workflowhub.eu/workflows/650?version=1, https://workflowhub.eu/workflows/651?version=1, https://workflowhub.eu/workflows/652?version=1, https://workflowhub.eu/workflows/653?version=1 |
microbiome/general-tutorial, microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short, sequence-analysis/Manage_AB1_Sanger |
True |
False |
|
motus |
mereg_mOTUs_tables, motus_profiler |
txt, biom1, bam_no_index |
Tool for profiling the abundance of microbial taxa. |
2024-09-06 |
https://github.com/motu-tool/mOTUs |
3.1.0 |
motus |
3.1.0 |
Up-to-date |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Metagenomics |
Metagenomics |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs |
https://github.com/bgruening/galaxytools/tree/master/tools/motus |
mOTUs |
Metagenomic operational taxonomic units (mOTUs) |
Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
40 |
40 |
377 |
377 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
377 |
377 |
40 |
40 |
|
|
True |
False |
|
mrbayes |
mrbayes |
txt |
A program for the Bayesian estimation of phylogeny. |
2015-12-04 |
|
1.0.2 |
mrbayes |
3.2.7 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
18 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
4 |
4 |
|
|
True |
False |
|
msconvert |
msconvert |
|
msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container |
2015-01-24 |
http://proteowizard.sourceforge.net/tools.shtml |
3.0.20287 |
|
|
To update |
Proteomics |
Filtering, Formatting |
Filtering, Formatting |
Proteomics, Proteomics experiment |
Proteomics, Proteomics experiment |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert |
msconvert |
msConvert |
msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
550 |
604 |
58574 |
66339 |
133 |
133 |
2254 |
2254 |
76 |
76 |
4844 |
4844 |
108 |
113 |
7765 |
7906 |
81343 |
73437 |
926 |
867 |
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metabolomics/gc_ms_with_xcms, microbiome/clinical-mp-2-discovery, proteomics/DIA_Analysis_OSW, proteomics/clinical-mp-2-discovery, proteomics/encyclopedia, proteomics/metaquantome-data-creation, proteomics/neoantigen-peptide-verification, proteomics/protein-id-oms |
True |
False |
|
msstatstmt |
msstatstmt |
txt, tabular, pdf |
MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling |
2021-01-20 |
http://msstats.org/msstatstmt/ |
2.0.0 |
bioconductor-msstatstmt |
2.10.0 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt |
|
|
|
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
113 |
113 |
844 |
844 |
10 |
10 |
47 |
47 |
18 |
18 |
693 |
693 |
0 |
0 |
0 |
0 |
1584 |
1584 |
141 |
141 |
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microbiome/clinical-mp-5-data-interpretation, proteomics/clinical-mp-5-data-interpretation, proteomics/maxquant-msstats-tmt |
True |
False |
|
msstatstmt |
msstats |
txt, tabular, pdf |
MSstats tool for analyzing mass spectrometry proteomic datasets |
2020-07-25 |
https://github.com/MeenaChoi/MSstats |
4.0.0 |
bioconductor-msstats |
4.18.1 |
To update |
Proteomics |
Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling |
Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling |
Proteomics, Proteomics experiment, Protein expression |
Proteomics, Proteomics experiment, Protein expression |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats |
msstatstmt |
MSstatsTMT |
Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling |
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
800 |
803 |
2969 |
3004 |
283 |
283 |
1456 |
1456 |
99 |
99 |
1605 |
1605 |
0 |
0 |
0 |
0 |
6065 |
6030 |
1185 |
1182 |
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proteomics/DIA_Analysis_MSstats, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq |
True |
False |
|
multigsea |
multigsea |
tabular |
GSEA-based pathway enrichment analysis for multi-omics data |
2023-06-07 |
https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html |
1.12.0 |
bioconductor-multigsea |
1.16.0 |
To update |
Transcriptomics, Proteomics, Statistics, Single Cell |
Gene-set enrichment analysis, Aggregation, Pathway analysis |
Gene-set enrichment analysis, Aggregation, Pathway analysis |
Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules |
Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea |
multiGSEA |
multiGSEA |
A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. |
|
0 |
1 |
1 |
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0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
65 |
65 |
212 |
212 |
0 |
0 |
0 |
0 |
5 |
5 |
46 |
46 |
0 |
0 |
0 |
0 |
258 |
258 |
70 |
70 |
https://workflowhub.eu/workflows/1388?version=1 |
proteomics/multiGSEA-tutorial |
True |
False |
|
multiqc |
multiqc |
html, tabular |
MultiQC aggregates results from bioinformatics analyses across many samples into a single report |
2017-09-21 |
http://multiqc.info/ |
1.33 |
multiqc |
1.33 |
Up-to-date |
Fastq Manipulation, Statistics, Visualization |
Validation, Sequencing quality control |
Sequencing quality control |
Sequencing, Bioinformatics, Sequence analysis, Genomics |
Sequencing, Bioinformatics, Sequence analysis, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc |
multiqc |
MultiQC |
MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. |
|
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1 |
1 |
1 |
0 |
0 |
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0 |
1 |
1 |
1 |
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0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
24162 |
26916 |
223019 |
248625 |
32289 |
38522 |
203104 |
241071 |
7040 |
7764 |
49577 |
54957 |
2276 |
2280 |
43768 |
43966 |
588619 |
519468 |
75482 |
65767 |
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assembly/assembly-with-preprocessing, assembly/general-introduction, assembly/hybrid_denovo_assembly, assembly/largegenome, assembly/unicycler-assembly, contributing/create-new-tutorial-content, ecology/ENA_Biodiv_submission, ecology/ref-based-rad-seq, epigenetics/cut_and_run, galaxy-interface/workflow-automation, galaxy-interface/workflow-fairification, genome-annotation/crispr-screen, introduction/galaxy-intro-ngs-data-managment, introduction/vsi_qc, microbiome/host-removal, microbiome/mags-building, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/mgnify-amplicon, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/mapping, sequence-analysis/quality-control, single-cell/scrna-preprocessing, single-cell/scrna-preprocessing-tenx, transcriptomics/differential-isoform-expression, transcriptomics/full-de-novo, transcriptomics/minerva-pathways, transcriptomics/mirna-target-finder, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts, variant-analysis/exome-seq, variant-analysis/sars-cov-2, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants, variant-analysis/tb-variant-analysis |
True |
False |
|
mykrobe |
mykrobe_predict |
csv |
Antibiotic resistance predictions |
2017-12-18 |
https://github.com/Mykrobe-tools/mykrobe |
0.10.0 |
mykrobe |
0.13.0 |
To update |
Sequence Analysis |
Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming |
Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming |
Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics |
Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe |
Mykrobe |
Mykrobe |
Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
mykrobe_parser |
mykrobe_parseR |
csv |
RScript to parse the results of mykrobe predictor. |
2018-09-28 |
https://github.com/phac-nml/mykrobe-parser |
0.1.4.1 |
r-base |
|
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/mykrobe-parser |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
mz_to_sqlite |
mz_to_sqlite |
mz.sqlite |
Creates a SQLite database for proteomics data |
2015-06-01 |
https://github.com/galaxyproteomics/mzToSQLite |
2.1.1+galaxy0 |
mztosqlite |
2.1.1 |
To update |
Proteomics |
Conversion, Peptide database search |
Conversion, Peptide database search |
Proteomics, Biological databases |
Proteomics, Biological databases |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite |
mztosqlite |
mzToSQLite |
Convert proteomics data files into a SQLite databaseExtract data from proteomics mzIdentML and mass spec scan files: mzML, MGF, etc and store in a SQLite database.The intended purpose is to provide a Galaxy dataset that can support an interactive Galaxy visualization plugin. |
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
136 |
146 |
868 |
959 |
17 |
17 |
83 |
83 |
18 |
18 |
336 |
336 |
0 |
0 |
0 |
0 |
1378 |
1287 |
181 |
171 |
https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=2a7e63d1cc583002, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e, https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2, https://workflowhub.eu/workflows/1429?version=1 |
proteomics/proteogenomics-dbsearch |
True |
False |
|
nanocompore |
nanocompore_db, nanocompore_sampcomp |
tabular, tar, txt |
Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. |
2020-04-27 |
https://nanocompore.rna.rocks/ |
1.0.0rc3.post2 |
nanocompore |
1.0.4 |
To update |
Sequence Analysis |
Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting |
PolyA signal detection, Genotyping, k-mer counting |
Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites |
Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore |
Nanocompore |
Nanocompore |
RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro |
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7 |
27 |
839 |
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5 |
5 |
365 |
371 |
0 |
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1210 |
392 |
12 |
10 |
https://usegalaxy.eu/published/workflow?id=778923dd04996e07, https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d |
|
True |
False |
|
nanoplot |
nanoplot |
html, tabular |
Plotting tool for long read sequencing data and alignments |
2018-09-24 |
https://github.com/wdecoster/NanoPlot |
1.46.2 |
nanoplot |
1.46.2 |
Up-to-date |
Visualization |
Scatter plot plotting, Box-Whisker plot plotting |
Scatter plot plotting, Box-Whisker plot plotting |
Genomics |
Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot |
nanoplot |
NanoPlot |
NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences |
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7663 |
7942 |
168514 |
173861 |
4903 |
5029 |
72856 |
74900 |
2940 |
2983 |
25741 |
26566 |
295 |
297 |
3814 |
3828 |
279155 |
270925 |
16251 |
15801 |
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assembly/assembly-with-preprocessing, assembly/chloroplast-assembly, assembly/largegenome, assembly/mrsa-nanopore, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore, sequence-analysis/quality-control |
True |
False |
|
nanopolishcomp |
nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate |
tabular, txt, bed |
NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. |
2020-04-27 |
https://a-slide.github.io/NanopolishComp |
0.6.11 |
nanopolishcomp |
0.6.12 |
To update |
Sequence Analysis |
Methylation analysis, Collapsing methods |
Methylation analysis, Collapsing methods |
Sequence analysis, Sequencing, Genetic variation |
Sequence analysis, Sequencing, Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp |
nanopolishcomp |
NanopolishComp |
NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. |
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38 |
709 |
1129 |
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1 |
1 |
1 |
1 |
1130 |
710 |
39 |
37 |
https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d |
|
True |
False |
|
ncbi_blast_plus |
blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper |
tabular, txt, fasta, maskinfo-asn1, data, blastdbd, pssm-asn1 |
NCBI BLAST+ |
2013-09-23 |
https://blast.ncbi.nlm.nih.gov/ |
2.16.0 |
blast |
2.17.0 |
To update |
Sequence Analysis |
|
|
|
|
devteam |
https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus |
https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus |
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4564 |
5012 |
608297 |
687163 |
5091 |
6262 |
690841 |
770815 |
1316 |
1731 |
262398 |
287817 |
159 |
164 |
12993 |
13154 |
1758949 |
1574529 |
13169 |
11130 |
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https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1, https://workflowhub.eu/workflows/645?version=16, https://workflowhub.eu/workflows/655?version=1 |
assembly/assembly-decontamination, data-science/online-resources-gene, ecology/ENA_Biodiv_submission, ecology/Obitools-metabarcoding, ecology/eDNA-taxonomic-analysis, genome-annotation/functional, proteomics/neoantigen-peptide-verification, proteomics/proteogenomics-novel-peptide-analysis, sequence-analysis/Manage_AB1_Sanger, sequence-analysis/ncbi-blast-against-the-madland, sequence-analysis/viral_primer_design |
True |
False |
|
ncbi_egapx |
ncbi_egapx |
gff |
Eukaryotic Genome Annotation Pipeline - External (EGAPx) |
2024-08-19 |
https://github.com/ncbi/egapx |
0.5.0 |
|
|
To update |
Genome annotation |
|
|
|
|
richard-burhans |
https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx |
https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx |
|
|
|
|
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
7 |
7 |
49 |
49 |
1037 |
1037 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1044 |
1044 |
51 |
51 |
https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=951575e9a352301c, https://usegalaxy.org/published/workflow?id=ce488732866ba48f, https://usegalaxy.org/published/workflow?id=e93a0522ec3a35e6 |
|
True |
False |
|
ncbi_fcs_gx |
ncbi_fcs_gx |
tabular, fasta |
FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). |
2023-09-21 |
https://github.com/ncbi/fcs-gx |
0.5.5 |
ncbi-fcs-gx |
0.5.5 |
Up-to-date |
Sequence Analysis |
Sequence assembly validation, Sequence trimming, Sequence contamination filtering |
Sequence assembly validation, Sequence trimming, Sequence contamination filtering |
Sequence analysis, Sequence assembly |
Sequence analysis, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx |
ncbi_fcs |
NCBI fcs |
The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
175 |
175 |
2259 |
2259 |
485 |
485 |
26859 |
26859 |
27 |
27 |
955 |
955 |
1 |
1 |
9 |
9 |
30082 |
30082 |
688 |
688 |
https://usegalaxy.eu/published/workflow?id=01d42b604ab92d49, https://usegalaxy.eu/published/workflow?id=c36560c74416fbbf, https://usegalaxy.eu/published/workflow?id=e035ac55551b2744, https://usegalaxy.org/published/workflow?id=529b410bd03b66aa, https://usegalaxy.org/published/workflow?id=5d1cc6450f699345, https://usegalaxy.org/published/workflow?id=927b8f90ad9603a7, https://workflowhub.eu/workflows/645?version=16 |
sequence-analysis/ncbi-fcs |
True |
False |
|
newick_utils |
newick_display |
svg |
Perform operations on Newick trees |
2018-10-01 |
https://github.com/tjunier/newick_utils |
1.6+galaxy1 |
newick_utils |
1.6 |
To update |
Visualization, Metagenomics |
Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction |
|
Phylogeny, Genomics, Computer science |
Phylogeny, Genomics, Computer science |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils |
newick_utilities |
Newick Utilities |
The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1756 |
1893 |
51682 |
53373 |
2196 |
2332 |
18983 |
20195 |
1114 |
1145 |
9635 |
9912 |
48 |
49 |
310 |
312 |
83792 |
80610 |
5419 |
5114 |
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evolution/abc_intro_phylo, microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short, microbiome/pathogen-detection-from-nanopore-foodborne-data |
True |
False |
|
nextclade |
nextalign, nextclade |
fasta, csv, tabular, json |
Identify differences between your sequences and a reference sequence used by Nextstrain |
2021-03-29 |
https://github.com/nextstrain/nextclade |
2.7.0 |
nextalign |
2.14.0 |
To update |
Sequence Analysis |
Methylation analysis, Variant calling |
Methylation analysis, Variant calling |
Genomics, Sequence analysis, Cladistics |
Genomics, Cladistics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade |
nextclade |
Nextclade |
Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. |
|
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
373 |
373 |
4718 |
4718 |
309 |
309 |
11632 |
11632 |
258 |
258 |
2460 |
2460 |
11 |
11 |
723 |
723 |
19533 |
19533 |
951 |
951 |
https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=1d1ebdeddf23bdb9, https://usegalaxy.eu/published/workflow?id=3f046b416b10b871, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=5c15f251642bfa1f, https://usegalaxy.eu/published/workflow?id=74f19aff1b9cdd6b, https://usegalaxy.eu/published/workflow?id=9feebfc6c34da287, https://usegalaxy.fr/published/workflow?id=2345fad7dac13daa, https://usegalaxy.fr/published/workflow?id=591c57173e259ca6, https://usegalaxy.fr/published/workflow?id=e4735d214a68b790, https://usegalaxy.fr/published/workflow?id=feb57548b3ce914d, https://usegalaxy.org.au/published/workflow?id=7563b3ef697a69fd, https://usegalaxy.org.au/published/workflow?id=af12a3ec85859563, https://usegalaxy.org/published/workflow?id=0fa2ce12c2874b1d, https://usegalaxy.org/published/workflow?id=426e3951dac0704e, https://usegalaxy.org/published/workflow?id=4b41a8247f52c463, https://usegalaxy.org/published/workflow?id=8b81b9a3b49bbf98, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://workflowhub.eu/workflows/155?version=6, https://workflowhub.eu/workflows/520?version=1 |
variant-analysis/sars-cov-2-variant-discovery |
True |
False |
|
nonpareil |
nonpareil |
tabular, txt, json |
Estimate average coverage in metagenomic datasets |
2017-11-03 |
http://nonpareil.readthedocs.io |
3.5.5 |
nonpareil |
3.5.5 |
Up-to-date |
Metagenomics |
Operation |
Operation |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil |
nonpareil |
nonpareil |
Estimate metagenomic coverage and sequence diversity |
|
1 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
16 |
19 |
105 |
195 |
23 |
26 |
122 |
168 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
363 |
227 |
45 |
39 |
|
|
True |
False |
|
nugen_nudup |
nugen_nudup |
bam, txt |
Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. |
2016-11-18 |
https://github.com/tecangenomics/nudup |
2.3.3 |
nudup |
2.3.3 |
Up-to-date |
SAM, Metagenomics, Sequence Analysis, Transcriptomics |
Duplication detection, Sequence analysis |
Duplication detection, Sequence analysis |
Sequencing, Genomics |
Sequencing, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup |
nudup |
NuDup |
Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
obitools |
obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq |
auto, txt, tabular |
OBITools is a set of programs developed to simplify the manipulation of sequence files |
2017-03-22 |
http://metabarcoding.org/obitools |
1.2.13 |
obitools |
1.2.13 |
Up-to-date |
Sequence Analysis |
Sequence analysis, Sequence analysis |
Sequence analysis, Sequence analysis |
Sequence analysis, DNA, Sequencing |
Sequence analysis, DNA, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools |
obitools |
OBITools |
Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. |
|
0 |
10 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
10 |
10 |
0 |
483 |
493 |
45330 |
45705 |
0 |
0 |
0 |
0 |
107 |
107 |
5011 |
5011 |
25 |
25 |
1398 |
1398 |
52114 |
51739 |
625 |
615 |
https://usegalaxy.eu/published/workflow?id=513389e1a8c6bba9, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=edf7e2128f5aef8d, https://usegalaxy.org.au/published/workflow?id=470eb26144325590, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/655?version=1 |
ecology/Obitools-metabarcoding |
True |
False |
|
omark |
omark |
txt, omq, pdf, png, sum, ump |
Proteome quality assessment software |
2023-11-15 |
https://github.com/DessimozLab/OMArk |
0.3.1 |
|
|
To update |
Sequence Analysis |
Sequence assembly validation, Differential protein expression profiling |
Sequence assembly validation, Differential protein expression profiling |
Proteomics, Sequence analysis, Statistics and probability |
Proteomics, Sequence analysis, Statistics and probability |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark |
omark |
OMArk |
OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
89 |
89 |
707 |
707 |
17 |
17 |
44 |
44 |
6 |
6 |
11 |
11 |
15 |
15 |
347 |
347 |
1109 |
1109 |
127 |
127 |
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genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation, genome-annotation/helixer |
True |
False |
|
openms |
AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter |
tabular, input, xml, mzml, html, idxml, consensusxml, traml, text, featurexml, fasta, mzq, trafoxml, txt, mzid, data, png, qcml, msp |
OpenMS in version 2.1. |
2015-02-28 |
|
2.1.0 |
openms |
3.5.0 |
To update |
Proteomics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/openms |
https://github.com/bgruening/galaxytools/tree/master/tools/openms |
|
|
|
|
7 |
34 |
135 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
27 |
135 |
134 |
0 |
583 |
698 |
30109 |
114383 |
10 |
10 |
417 |
417 |
33 |
34 |
1321 |
1325 |
0 |
0 |
0 |
0 |
116125 |
31847 |
742 |
626 |
https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=68edbb8eec38ad00, https://usegalaxy.eu/published/workflow?id=7463b26aab6a965d, https://usegalaxy.eu/published/workflow?id=86d50bbaaa3936dc, https://usegalaxy.eu/published/workflow?id=a2cdadcd549c9c3c, https://usegalaxy.eu/published/workflow?id=afb138fc03ca61a8, https://usegalaxy.eu/published/workflow?id=d55df785d4c71876, https://usegalaxy.eu/published/workflow?id=da10c475c83c5469, https://usegalaxy.eu/published/workflow?id=e9e41c23261d4ac5, https://usegalaxy.eu/published/workflow?id=eaf4d8f8fb3e683d, https://usegalaxy.org.au/published/workflow?id=03efeb2948494130, https://usegalaxy.org.au/published/workflow?id=049c52f685984dec, https://usegalaxy.org.au/published/workflow?id=236e0f306916149b, https://usegalaxy.org.au/published/workflow?id=33922db405a97cbb, https://usegalaxy.org.au/published/workflow?id=59c9a6efaf57ce35, https://usegalaxy.org.au/published/workflow?id=65a659982f955743, https://usegalaxy.org.au/published/workflow?id=7cddb345877f08bf, https://usegalaxy.org.au/published/workflow?id=88fa3e250db2d70e, https://usegalaxy.org.au/published/workflow?id=8c874ea77827448c, https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5, https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc, https://usegalaxy.org/published/workflow?id=0775ff66d1bc04b5, https://usegalaxy.org/published/workflow?id=9865fee6c68fc201, https://usegalaxy.org/published/workflow?id=f9048d9678e21f36, https://workflowhub.eu/workflows/1394?version=1, https://workflowhub.eu/workflows/1399?version=1, https://workflowhub.eu/workflows/1421?version=1, https://workflowhub.eu/workflows/1424?version=1, https://workflowhub.eu/workflows/1434?version=1, https://workflowhub.eu/workflows/1438?version=1, https://workflowhub.eu/workflows/1446?version=1, https://workflowhub.eu/workflows/1449?version=1, https://workflowhub.eu/workflows/1452?version=1, https://workflowhub.eu/workflows/1463?version=1, https://workflowhub.eu/workflows/613?version=2 |
proteomics/DIA_Analysis_OSW, proteomics/DIA_lib_OSW, proteomics/database-handling, proteomics/ntails, proteomics/protein-id-oms, proteomics/protein-id-sg-ps, proteomics/protein-quant-sil |
True |
False |
|
orfipy |
orfipy |
bed6, bed12, fasta |
Galaxy wrapper for ORFIPY |
2022-04-07 |
https://github.com/urmi-21/orfipy |
0.0.4 |
orfipy |
0.0.4 |
Up-to-date |
Sequence Analysis |
Coding region prediction, Database search, Transcriptome assembly, De-novo assembly |
Coding region prediction, Database search, Transcriptome assembly, De-novo assembly |
Computer science, RNA-Seq, Transcriptomics, Small molecules |
Computer science, RNA-Seq, Transcriptomics, Small molecules |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy |
orfipy |
orfipy |
A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. |
|
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
172 |
172 |
1509 |
1509 |
343 |
343 |
2776 |
2776 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4285 |
4285 |
515 |
515 |
https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df |
genome-annotation/gene-centric |
True |
False |
|
orthofinder |
orthofinder_onlygroups |
txt, tsv, newick |
Accurate inference of orthologous gene groups made easy |
2017-05-22 |
https://github.com/davidemms/OrthoFinder |
2.5.5 |
orthofinder |
3.1.2 |
To update |
Phylogenetics, Sequence Analysis |
Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment |
Genome comparison, Genome alignment |
Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis |
Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder |
OrthoFinder |
OrthoFinder |
OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
801 |
801 |
3870 |
3870 |
0 |
0 |
0 |
0 |
133 |
133 |
1450 |
1450 |
36 |
36 |
221 |
221 |
5541 |
5541 |
970 |
970 |
https://usegalaxy.eu/published/workflow?id=d8492b49aed84d4f, https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c |
|
True |
False |
|
pacu |
pacu_map, pacu_snp |
bam, html |
PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. |
2024-08-13 |
https://github.com/BioinformaticsPlatformWIV-ISP/PACU |
0.0.5 |
pacu_snp |
1.0.0 |
To update |
Sequence Analysis, Phylogenetics |
Clustering |
Clustering |
Phylogenetics, Sequence analysis |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu |
pacu |
PACU |
PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
19 |
223 |
223 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
223 |
223 |
19 |
19 |
|
|
True |
False |
|
pal2nal |
pal2nal |
txt, html |
Wraps PAL2NAL to convert protein alignments and nucleotide FASTA into codon-aware alignments. |
2025-11-09 |
http://www.bork.embl.de/pal2nal |
|
pal2nal |
14.1 |
To update |
Sequence Analysis, Phylogenetics |
|
|
|
|
iuc |
https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pal2nal |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
pampa |
pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm |
tabular, txt |
Tools to compute and analyse biodiversity metrics |
2020-06-06 |
|
0.0.2 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/ColineRoyaux/PAMPA-Galaxy |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA |
|
|
|
|
0 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
4 |
0 |
50 |
53 |
1997 |
2045 |
0 |
0 |
0 |
0 |
26 |
26 |
1141 |
1141 |
1 |
1 |
1 |
1 |
3187 |
3139 |
80 |
77 |
https://usegalaxy.eu/published/workflow?id=428be4c7d1fd828f, https://usegalaxy.eu/published/workflow?id=7c45c90fffe40aca, https://usegalaxy.eu/published/workflow?id=d33ab07e4cf44f8c, https://workflowhub.eu/workflows/1696?version=1 |
ecology/PAMPA-toolsuite-tutorial |
True |
False |
|
panaroo |
panaroo |
txt |
A Bacterial Pangenome Analysis Pipeline |
2025-02-28 |
https://github.com/gtonkinhill/panaroo/releases |
1.6.0 |
panaroo |
1.6.0 |
Up-to-date |
Sequence Analysis |
De-novo assembly, Genome assembly, Clustering |
De-novo assembly, Genome assembly, Clustering |
Workflows, Sequence assembly, Gene and protein families, Plant biology, Sequencing |
Workflows, Sequence assembly, Gene and protein families, Plant biology, Sequencing |
galaxy-australia |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo |
panaroo |
Panaroo |
Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
67 |
67 |
297 |
297 |
0 |
0 |
0 |
0 |
39 |
39 |
312 |
312 |
0 |
0 |
0 |
0 |
609 |
609 |
106 |
106 |
|
|
True |
False |
|
panta |
panta |
json, tsv, csv, txt, fasta |
Efficient inference of large prokaryotic pangenomes with PanTA. |
2025-09-15 |
https://github.com/amromics/panta |
1.0.1 |
panta |
1.0.1 |
Up-to-date |
Genome annotation, Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
peptideshaker |
fasta_cli, ident_params, peptide_shaker, search_gui |
fasta, json, zip, mzid, peptideshaker_archive, txt, tabular, searchgui_archive |
PeptideShaker and SearchGUI |
2015-01-31 |
http://compomics.github.io |
|
searchgui |
4.3.15 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker |
|
|
|
|
4 |
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
2 |
0 |
541 |
635 |
10278 |
19384 |
236 |
236 |
1790 |
1790 |
54 |
54 |
3790 |
3855 |
2 |
3 |
15 |
21 |
25050 |
15873 |
928 |
833 |
https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=0e0be913c3e27022, https://usegalaxy.eu/published/workflow?id=1706bfa819bbfa89, https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=249c7569b61fb349, https://usegalaxy.eu/published/workflow?id=2a7e63d1cc583002, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=4c81726bde25c36a, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6766bed39f614b7c, https://usegalaxy.eu/published/workflow?id=68967c922de149ae, https://usegalaxy.eu/published/workflow?id=6aca8a72626c521b, https://usegalaxy.eu/published/workflow?id=6b7b86756060659b, https://usegalaxy.eu/published/workflow?id=6bd8311554412c38, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=7463b26aab6a965d, https://usegalaxy.eu/published/workflow?id=78e1769f1dcb797b, https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=8fc1ea9e94bc723d, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=9c0132dd81297afe, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=a4d6b9dc6b396933, https://usegalaxy.eu/published/workflow?id=a657b412b37b971b, https://usegalaxy.eu/published/workflow?id=b73fa5f8c0403454, https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=c6b6ba35e5b6500a, https://usegalaxy.eu/published/workflow?id=c750484145c9903b, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=d1d5a6bd6571d47f, https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2, https://usegalaxy.eu/published/workflow?id=d5756e3ebfa285ef, https://usegalaxy.eu/published/workflow?id=d9e7a940b2d410bc, https://usegalaxy.eu/published/workflow?id=df926c5ab8d27192, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=f34c76e2d8045725, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2, https://usegalaxy.org.au/published/workflow?id=33922db405a97cbb, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5, https://usegalaxy.org.au/published/workflow?id=f9f685d6150e48c5, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1394?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1399?version=1, https://workflowhub.eu/workflows/1429?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1443?version=1, https://workflowhub.eu/workflows/1450?version=1 |
microbiome/clinical-mp-2-discovery, proteomics/clinical-mp-2-discovery, proteomics/metaproteomics, proteomics/metaquantome-data-creation, proteomics/protein-id-sg-ps, proteomics/proteogenomics-dbsearch |
True |
False |
|
pfamscan |
pfamscan |
tabular |
Search a FASTA sequence against a library of Pfam HMM. |
2023-02-02 |
http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ |
1.6 |
pfam_scan |
1.6 |
Up-to-date |
Sequence Analysis |
Protein sequence analysis |
Protein sequence analysis |
Sequence analysis |
Sequence analysis |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan |
https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan |
pfamscan |
PfamScan |
This tool is used to search a FASTA sequence against a library of Pfam HMM. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
146 |
146 |
7522 |
7522 |
143 |
143 |
881 |
881 |
33 |
33 |
545 |
545 |
1 |
1 |
1 |
1 |
8949 |
8949 |
323 |
323 |
https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://workflowhub.eu/workflows/1688?version=1 |
transcriptomics/differential-isoform-expression |
True |
False |
|
phabox |
phabox_cherry, phabox_contamination, phabox_end_to_end, phabox_phagcn, phabox_phamer, phabox_phatyp, phabox_phavip, phabox_tree, phabox_votu |
tabular |
Identify and analyze phage contigs in metagenomic data |
2024-11-12 |
https://github.com/KennthShang/PhaBOX |
2.1.11 |
phabox |
2.1.13 |
To update |
Metagenomics |
Sequence assembly, Taxonomic classification, Visualisation |
Sequence assembly, Taxonomic classification, Visualisation |
Metagenomics, Microbial ecology, Sequence assembly, Taxonomy |
Metagenomics, Microbial ecology, Sequence assembly, Taxonomy |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phabox |
phabox |
PhaBOX |
Web server for identifying and characterizing phage contigs in metagenomic data. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
pharokka |
pharokka |
genbank, gff, zip |
rapid standardised annotation tool for bacteriophage genomes and metagenomes |
2023-02-14 |
https://github.com/gbouras13/pharokka |
1.3.2 |
\n pharokka\n |
|
To update |
Genome annotation |
Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly |
Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly |
Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA |
Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka |
pharokka |
Pharokka |
Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
766 |
766 |
16933 |
16933 |
1 |
1 |
21 |
21 |
117 |
117 |
1202 |
1202 |
0 |
0 |
0 |
0 |
18156 |
18156 |
884 |
884 |
https://usegalaxy.eu/published/workflow?id=62392daea25a3980 |
|
True |
False |
|
phi_toolkit_report |
phi_toolkit_report |
html |
Phage host interaction toolkit report generator |
2025-06-04 |
https://git.ufz.de/borimcor/phage-host-analysis |
0.2.0 |
bioconductor-biostrings |
2.78.0 |
To update |
Metagenomics |
|
|
|
|
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phi-toolkit |
|
|
|
|
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
https://usegalaxy.eu/published/workflow?id=c62d65832377e376 |
|
True |
False |
|
phyloseq |
phyloseq_add_rank_names, phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_bar, phyloseq_plot_ordination, phyloseq_plot_richness, phyloseq_tax_glom |
phyloseq, pdf, tabular |
Handling and analysis of high-throughput microbiome census data |
2022-03-03 |
https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html |
1.50.0 |
bioconductor-phyloseq |
1.50.0 |
Up-to-date |
Metagenomics |
Deposition, Analysis, Visualisation |
Deposition, Analysis, Visualisation |
Microbiology, Sequence analysis, Metagenomics |
Microbiology, Sequence analysis, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq |
phyloseq |
phyloseq |
Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. |
|
4 |
1 |
7 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
3 |
3 |
0 |
251 |
251 |
3161 |
3161 |
156 |
156 |
1022 |
1022 |
35 |
35 |
190 |
190 |
14 |
14 |
163 |
163 |
4536 |
4536 |
456 |
456 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=e3918808605cf8cd, https://usegalaxy.org/published/workflow?id=4faff660f6defa10, https://workflowhub.eu/workflows/1395?version=2 |
microbiome/dada-16S |
True |
False |
|
phyml |
phyml |
nhx, txt |
PhyML is a phylogeny software based on the maximum-likelihood principle. |
2019-05-27 |
http://www.atgc-montpellier.fr/phyml/ |
3.3.20220408 |
phyml |
3.3.20220408 |
Up-to-date |
Phylogenetics |
Phylogenetic tree generation (maximum likelihood and Bayesian methods) |
|
Phylogenetics, Bioinformatics, Phylogenetics |
Phylogenetics, Bioinformatics, Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml |
phyml |
PhyML |
Phylogenetic estimation software using Maximum Likelihood |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
286 |
335 |
2452 |
2654 |
0 |
0 |
0 |
0 |
215 |
240 |
1475 |
1564 |
79 |
79 |
334 |
334 |
4552 |
4261 |
654 |
580 |
https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0 |
|
True |
False |
|
picrust |
picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes |
tabular, nhx |
PICRUSt wrappers |
2016-11-08 |
https://picrust.github.io/picrust/ |
1.1.1 |
picrust |
1.1.4 |
To update |
Metagenomics |
Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding |
Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding |
Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing |
Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust |
picrust |
PICRUSt |
PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. |
|
0 |
6 |
5 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
0 |
44 |
63 |
562 |
1142 |
0 |
0 |
0 |
0 |
38 |
41 |
2348 |
2626 |
20 |
20 |
442 |
442 |
4210 |
3352 |
124 |
102 |
|
|
True |
False |
|
picrust2 |
picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions |
tabular |
PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States |
2021-07-09 |
https://github.com/picrust/picrust2/wiki |
2.5.3 |
picrust2 |
2.6.3 |
To update |
Metagenomics |
Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis |
Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis |
Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing |
Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 |
picrust2 |
PICRUSt2 |
PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. |
|
0 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
0 |
0 |
327 |
327 |
6432 |
6432 |
1 |
1 |
1 |
1 |
64 |
64 |
2888 |
2888 |
0 |
0 |
0 |
0 |
9321 |
9321 |
392 |
392 |
https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34 |
|
True |
False |
|
pimento |
pimento_are_there_primers, pimento_auto, pimento_choose_primer_cutoff, pimento_find_cutoffs, pimento_gen_bcv, pimento_std |
txt, fasta, tsv |
A PrIMEr infereNce TOolkit to facilitate large-scale calling of metabarcoding amplicon sequence variants. |
2025-08-04 |
https://github.com/EBI-Metagenomics/PIMENTO |
1.0.2 |
mi-pimento |
1.0.2 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento |
|
|
|
|
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1 |
|
|
True |
False |
|
pirate |
pirate |
txt, tsv, fasta, newick, gfa1, gff, pdf |
Pangenome Iterative Refinement and Threshold Evaluation. |
2026-01-31 |
https://github.com/SionBayliss/PIRATE |
1.0.5 |
pirate |
1.0.5 |
Up-to-date |
Sequence Analysis, Genome annotation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
plasclass |
plasclass |
tabular |
PlasClass is a tool to classify sequences of plasmid or chromosomal origin |
2025-07-31 |
https://github.com/Shamir-Lab/PlasClass |
0.1.1 |
plasclass |
0.1.1 |
Up-to-date |
Sequence Analysis |
Sequence classification, Sequence assembly, k-mer counting |
Sequence classification, Sequence assembly, k-mer counting |
Metagenomics, Sequence assembly, DNA, Metagenomic sequencing |
Metagenomics, Sequence assembly, DNA, Metagenomic sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass |
PlasClass |
PlasClass |
PlasClass is a tool for easy classification of sequences as either plasmid or chromosomal. For example, it can be used to classify the contigs in a (metagenomic) assembly. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
plasflow |
PlasFlow |
tabular, fasta |
PlasFlow - Prediction of plasmid sequences in metagenomic contigs. |
2018-09-05 |
https://github.com/smaegol/PlasFlow |
1.1.0 |
plasflow |
1.1.0 |
Up-to-date |
Sequence Analysis |
Sequence analysis |
Sequence analysis |
Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning |
Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow |
plasflow |
PlasFlow |
PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
876 |
1004 |
55069 |
56639 |
757 |
797 |
7929 |
8195 |
87 |
87 |
3496 |
3496 |
0 |
0 |
0 |
0 |
68330 |
66494 |
1888 |
1720 |
https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 |
microbiome/plasmid-metagenomics-nanopore |
True |
False |
|
plasmidfinder |
plasmidfinder |
json, fasta, tabular, txt |
"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" |
2022-09-19 |
https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ |
2.1.6 |
plasmidfinder |
2.1.6 |
Up-to-date |
Sequence Analysis |
Genome assembly, Scaffolding, Multilocus sequence typing |
Genome assembly, Scaffolding, Multilocus sequence typing |
Whole genome sequencing, Sequence assembly, Mapping, Probes and primers |
Whole genome sequencing, Sequence assembly, Mapping, Probes and primers |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder |
PlasmidFinder |
PlasmidFinder |
PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
1015 |
1015 |
35994 |
35994 |
623 |
623 |
11939 |
11939 |
211 |
211 |
3278 |
3278 |
48 |
48 |
10730 |
10730 |
61941 |
61941 |
1897 |
1897 |
https://usegalaxy.eu/published/workflow?id=1306ed083d91a852, https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=67ca17ab34b10772, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=13, https://workflowhub.eu/workflows/1513?version=1 |
genome-annotation/bacterial-genome-annotation |
True |
False |
|
plasmidspades |
plasmidspades |
fasta, tabular, txt |
Genome assembler for assemblying plasmid |
2016-06-06 |
|
1.1 |
spades |
4.2.0 |
To update |
Assembly |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
polypolish |
polypolish |
fasta, tabular, txt |
"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." |
2022-09-22 |
https://github.com/rrwick/Polypolish |
0.6.1 |
polypolish |
0.6.1 |
Up-to-date |
Sequence Analysis |
Genome assembly, Read mapping, Mapping assembly, Sequencing error detection |
Genome assembly, Read mapping, Mapping assembly, Sequencing error detection |
Sequence assembly, Sequence composition, complexity and repeats, Mapping |
Sequence assembly, Sequence composition, complexity and repeats, Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish |
Polypolish |
Polypolish |
Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
147 |
147 |
1066 |
1066 |
0 |
0 |
0 |
0 |
26 |
26 |
615 |
615 |
10 |
10 |
79 |
79 |
1760 |
1760 |
183 |
183 |
https://workflowhub.eu/workflows/1613?version=2 |
assembly/mrsa-nanopore |
True |
False |
|
ppanggolin |
ppanggolin_all, ppanggolin_msa, ppanggolin_projection, ppanggolin_rarefaction |
tsv, fasta, json, xml, html, csv, txt, h5, tar.gz, maf, tabular |
Microbial Partitioned PanGenome |
2025-01-22 |
https://github.com/labgem/PPanGGOLiN |
2.2.6 |
ppanggolin |
2.2.6 |
Up-to-date |
Genome annotation |
Rarefaction, Essential dynamics, Sequence assembly, Genome annotation |
Rarefaction, Essential dynamics, Sequence assembly, Genome annotation |
Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping |
Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin |
ppanggolin |
PPanGGOLiN |
PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species |
|
0 |
0 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
55 |
55 |
249 |
249 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
67 |
67 |
316 |
316 |
71 |
71 |
|
genome-annotation/bacterial-pangenomics |
True |
False |
|
prodigal |
prodigal |
genbank, fasta, tabular |
A protein-coding gene prediction software tool for bacterial and archaeal genomes |
2024-03-14 |
https://github.com/hyattpd/Prodigal |
2.6.3 |
prodigal |
2.6.3 |
Up-to-date |
Genome annotation |
Genome annotation |
Genome annotation |
Genomics, Sequence analysis |
Genomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal |
prodigal |
Prodigal |
Fast, reliable protein-coding gene prediction for prokaryotic genomes. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
611 |
611 |
6456 |
6456 |
0 |
0 |
0 |
0 |
70 |
70 |
1515 |
1515 |
19 |
19 |
1487 |
1487 |
9458 |
9458 |
700 |
700 |
https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://usegalaxy.org/published/workflow?id=d3c400275889ce4b, https://workflowhub.eu/workflows/1663?version=1, https://workflowhub.eu/workflows/2024?version=2 |
ecology/marine_omics_bgc |
True |
False |
|
prokka |
prokka |
gff3, genbank, fasta, asn1, txt, tabular |
Rapid annotation of prokaryotic genomes |
2016-10-07 |
http://github.com/tseemann/prokka |
1.14.6 |
prokka |
1.15.6 |
To update |
Sequence Analysis |
Gene prediction, Coding region prediction, Genome annotation |
Coding region prediction, Genome annotation |
Genomics, Model organisms, Virology |
Genomics, Model organisms, Virology |
crs4 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka |
prokka |
Prokka |
Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
10459 |
11098 |
819587 |
847581 |
14547 |
16587 |
462648 |
506432 |
5094 |
6142 |
199279 |
229418 |
422 |
424 |
7463 |
7481 |
1590912 |
1488977 |
34251 |
30522 |
https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=12653a1e65a20304, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=165089132248a0b0, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=a847773b563b2328, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=b1a799497c366eef, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=ce8bf03d3df24806, https://usegalaxy.eu/published/workflow?id=cf8591391a17a914, https://usegalaxy.eu/published/workflow?id=d92f9c33dded693f, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4, https://usegalaxy.eu/published/workflow?id=e8eb80ee09159bac, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=f141db5179ea8422, https://usegalaxy.eu/published/workflow?id=f97e6fe1fcbc53a7, https://usegalaxy.eu/published/workflow?id=fe43cf59e48bf556, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=33401b29d277b447, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=39c724282ee008e3, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=6c67e22d18566af3, https://usegalaxy.org.au/published/workflow?id=7c343e5b55474d19, https://usegalaxy.org.au/published/workflow?id=87cdeb05b1ebeab0, https://usegalaxy.org.au/published/workflow?id=8f7d5ebead46a6d0, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=b5403e4fff2961f9, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=e20172eb0f30d6cd, https://usegalaxy.org.au/published/workflow?id=f01be6a7685ac476, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org.au/published/workflow?id=fc664a96d8099652, https://usegalaxy.org/published/workflow?id=0795dd1d83662bae, https://usegalaxy.org/published/workflow?id=109092d8dbda4398, https://usegalaxy.org/published/workflow?id=1c7af480caf150bd, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=3cf46c167ccb374f, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=78d8b738f5715a8a, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=87b3305ea433b4e2, https://usegalaxy.org/published/workflow?id=88bc9aa7090875c1, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://usegalaxy.org/published/workflow?id=b43b72dcf5f7694d, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=e2ab3d3219a648a7, https://usegalaxy.org/published/workflow?id=e75bd7d392e65209, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://workflowhub.eu/workflows/1497?version=1, https://workflowhub.eu/workflows/1598?version=1, https://workflowhub.eu/workflows/1617?version=1, https://workflowhub.eu/workflows/1767?version=1 |
assembly/chloroplast-assembly, assembly/unicycler-assembly, genome-annotation/annotation-with-prokka |
True |
False |
|
promer |
promer4_substitutions |
tabular, fasta |
Aligns two sets of contigs and reports amino acid substitutions between them |
2019-12-14 |
https://github.com/phac-nml/promer |
1.2 |
python |
|
To update |
Assembly |
|
|
|
|
nml |
https://github.com/phac-nml/promer |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
proteinortho |
proteinortho, proteinortho_clustering, proteinortho_grab_proteins, proteinortho_summary |
tabular |
Proteinortho is a tool to detect orthologous proteins/genes within different species. |
2020-02-05 |
https://gitlab.com/paulklemm_PHD/proteinortho |
6.3.6 |
proteinortho |
6.3.6 |
Up-to-date |
Proteomics |
Sequence clustering, Sequence analysis |
Sequence clustering, Sequence analysis |
Comparative genomics |
Comparative genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho |
proteinortho |
Proteinortho |
Proteinortho is a tool to detect orthologous genes within different species |
|
0 |
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
0 |
432 |
463 |
5028 |
5485 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
23 |
23 |
5508 |
5051 |
467 |
436 |
https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1 |
ecology/phylogeny-data-prep |
True |
False |
|
pycoqc |
pycoqc |
html, json |
QC metrics for ONT Basecalling |
2021-03-02 |
https://github.com/tleonardi/pycoQC |
2.5.2 |
pycoqc |
2.5.2 |
Up-to-date |
Nanopore |
Sequencing quality control, Statistical calculation |
Sequencing quality control, Statistical calculation |
Sequence analysis, Data quality management, Sequencing |
Sequence analysis, Data quality management, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc |
pycoqc |
pycoQC |
PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
832 |
832 |
23549 |
23549 |
1182 |
1182 |
4440 |
4440 |
606 |
606 |
1143 |
1143 |
158 |
158 |
322 |
322 |
29454 |
29454 |
2778 |
2778 |
https://usegalaxy.eu/published/workflow?id=97e28207076e1e98, https://usegalaxy.org.au/published/workflow?id=01393562b82f1884, https://usegalaxy.org.au/published/workflow?id=0d1d4392c3042fbd, https://usegalaxy.org.au/published/workflow?id=31dbe7344d72b903, https://usegalaxy.org.au/published/workflow?id=364025bd13970867, https://usegalaxy.org.au/published/workflow?id=419e09e4a2fa6d38, https://usegalaxy.org.au/published/workflow?id=5f4e164c18810cca, https://usegalaxy.org.au/published/workflow?id=866b69c5ee6601fe, https://usegalaxy.org.au/published/workflow?id=8fe84de499e96485, https://usegalaxy.org.au/published/workflow?id=98f285d6f0253b81, https://usegalaxy.org.au/published/workflow?id=c87b645aedfb857d, https://usegalaxy.org.au/published/workflow?id=da3d4b39b0d655e7, https://usegalaxy.org.au/published/workflow?id=ed43af416c6a7d3b, https://usegalaxy.org.au/published/workflow?id=fdf32312e8567093 |
sequence-analysis/quality-control |
True |
False |
|
pygenometracks |
pygenomeTracks |
png |
pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. |
2018-06-08 |
https://github.com/deeptools/pyGenomeTracks |
3.9 |
pygenometracks |
3.9 |
Up-to-date |
Visualization |
Visualisation, Formatting |
Visualisation, Formatting |
Model organisms, Imaging, Workflows |
Model organisms, Imaging, Workflows |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks |
pygenometracks |
pyGenomeTracks |
reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1301 |
1446 |
13377 |
16146 |
1427 |
1472 |
11997 |
12438 |
210 |
210 |
5014 |
5054 |
44 |
44 |
81 |
81 |
33719 |
30469 |
3172 |
2982 |
https://usegalaxy.eu/published/workflow?id=02655d0e4af0ee0d, https://usegalaxy.eu/published/workflow?id=2a9c812f59b7b36c, https://usegalaxy.eu/published/workflow?id=4464d3b0fc782a1a, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=506a451679fe25b4, https://usegalaxy.eu/published/workflow?id=72201ffaf488f278, https://usegalaxy.eu/published/workflow?id=9843ae66c3b367b7, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9f8a93cfffb31cd6, https://usegalaxy.eu/published/workflow?id=9fc8b89954c04ee1, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=f394d1b12779ba41, https://usegalaxy.org.au/published/workflow?id=13ce18408ee7acc9, https://usegalaxy.org.au/published/workflow?id=99821674db7682bb, https://usegalaxy.org/published/workflow?id=06eaa5b141fe7a08, https://usegalaxy.org/published/workflow?id=0bc1b8888d8b20c4, https://usegalaxy.org/published/workflow?id=1dc312e3fba9f810, https://usegalaxy.org/published/workflow?id=4998f171ec922c7d, https://usegalaxy.org/published/workflow?id=582f3de3971fc38c, https://usegalaxy.org/published/workflow?id=7353afb9301780e5, https://usegalaxy.org/published/workflow?id=b31ab9e76409a9b7, https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://usegalaxy.org/published/workflow?id=f13432eef7ac28e9, https://usegalaxy.org/published/workflow?id=f80b80aa7fb196ba, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1568?version=2, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1847?version=1, https://workflowhub.eu/workflows/420?version=3 |
epigenetics/atac-seq, epigenetics/hicexplorer, transcriptomics/differential-isoform-expression, transcriptomics/ref-based |
True |
False |
|
qiime |
qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file |
fasta, txt, tabular, html, pdf, fastq, biom1, png, svg, nhx, qual |
QIIME to perform microbial community analysis |
2017-01-16 |
http://www.qiime.org |
|
qiime |
1.9.1 |
To update |
Metagenomics |
Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control |
Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control |
Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics |
Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core |
qiime_core |
qiime_core |
QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. |
|
0 |
0 |
32 |
32 |
0 |
0 |
0 |
0 |
0 |
0 |
32 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
31 |
0 |
418 |
483 |
34279 |
42817 |
1 |
1 |
1617 |
1617 |
1 |
1 |
2 |
16 |
17 |
17 |
4517 |
4550 |
49000 |
40415 |
502 |
437 |
https://usegalaxy.eu/published/workflow?id=3acfb87be6db2303, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1 |
sequence-analysis/Manage_AB1_Sanger |
True |
False |
|
qiime |
qiime_collapse_samples, qiime_make_otu_table |
biom1, tabular |
QIIME to perform microbial community analysis |
2017-01-16 |
http://www.qiime.org |
|
qiime |
1.9.1 |
To update |
Metagenomics |
Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control |
Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control |
Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics |
Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on |
qiime_add_on |
qiime_add_on |
QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
183 |
242 |
2193 |
2749 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
9 |
9 |
18 |
18 |
2769 |
2213 |
252 |
193 |
https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4 |
|
True |
False |
|
qiime2 |
qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq |
qza |
|
2022-08-26 |
https://qiime2.org |
2026.1.0+dist.h02a552c2 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
2 |
2 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
636 |
636 |
61165 |
61165 |
813 |
813 |
58124 |
58124 |
228 |
228 |
10152 |
10152 |
62 |
62 |
2237 |
2237 |
131678 |
131678 |
1739 |
1739 |
https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, https://usegalaxy.eu/published/workflow?id=ca5da5179cefec8b, https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8, https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e, https://usegalaxy.org.au/published/workflow?id=3c1bf73067334071, https://usegalaxy.org.au/published/workflow?id=543001c51567b438, https://usegalaxy.org.au/published/workflow?id=57aa23f4f0418a07, https://usegalaxy.org.au/published/workflow?id=cddd668a29b1488a, https://usegalaxy.org.au/published/workflow?id=f946d722f7c27479, https://usegalaxy.org/published/workflow?id=0dc387dc861bdb61, https://usegalaxy.org/published/workflow?id=4ca9319c98be08f8, https://usegalaxy.org/published/workflow?id=685b0de4c31f6695, https://usegalaxy.org/published/workflow?id=76b2c4762dd61d03, https://usegalaxy.org/published/workflow?id=7aa87e7f9cfdae78, https://usegalaxy.org/published/workflow?id=a7cc1038b14f2201, https://usegalaxy.org/published/workflow?id=b335f75495dab9b4, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://usegalaxy.org/published/workflow?id=c6b6524108f53688, https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318, https://workflowhub.eu/workflows/893?version=3 |
|
True |
False |
|
qiime2 |
qiime2__quality_filter__q_score |
qza |
|
2022-08-26 |
https://github.com/qiime2/q2-quality-filter |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
25 |
25 |
55 |
55 |
16 |
16 |
39 |
39 |
7 |
7 |
90 |
90 |
13 |
13 |
21 |
21 |
205 |
205 |
61 |
61 |
|
|
True |
False |
|
qiime2 |
qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_bv_brc_genome_features, qiime2__rescript__get_bv_brc_genomes, qiime2__rescript__get_bv_brc_metadata, qiime2__rescript__get_eukaryome_data, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_midori2_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_pr2_data, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_reads, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment |
qza, qzv |
|
2024-04-25 |
https://github.com/nbokulich/RESCRIPt |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
18 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
6 |
6 |
|
|
True |
False |
|
qiime2 |
qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize |
qza, qzv |
|
2022-08-26 |
https://github.com/qiime2/q2-sample-classifier |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
15 |
15 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
0 |
0 |
5 |
5 |
30 |
30 |
17 |
17 |
47 |
47 |
5 |
5 |
6 |
6 |
1 |
1 |
4 |
4 |
87 |
87 |
28 |
28 |
|
|
True |
False |
|
qiime2 |
qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds |
qza |
|
2022-08-26 |
https://github.com/qiime2/q2-phylogeny |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
12 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
0 |
0 |
167 |
167 |
880 |
880 |
93 |
93 |
338 |
338 |
66 |
66 |
373 |
373 |
13 |
13 |
91 |
91 |
1682 |
1682 |
339 |
339 |
https://usegalaxy.eu/published/workflow?id=7c07e87c77dcee05 |
|
True |
False |
|
qiime2 |
qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate |
qza, qzv |
|
2022-08-26 |
https://github.com/qiime2/q2-metadata |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
331 |
331 |
2227 |
2227 |
292 |
292 |
1317 |
1317 |
94 |
94 |
744 |
744 |
39 |
39 |
269 |
269 |
4557 |
4557 |
756 |
756 |
https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3 |
|
True |
False |
|
qiime2 |
qiime2__stats__alpha_group_significance, qiime2__stats__collate_stats, qiime2__stats__facet_across, qiime2__stats__facet_within, qiime2__stats__mann_whitney_u, qiime2__stats__mann_whitney_u_facet, qiime2__stats__plot_rainclouds, qiime2__stats__prep_alpha_distribution, qiime2__stats__wilcoxon_srt, qiime2__stats__wilcoxon_srt_facet |
qza, qzv |
|
2024-10-30 |
https://github.com/qiime2/q2-stats |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
qiime2 |
qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads |
qza, qzv |
|
2022-08-26 |
https://github.com/qiime2/q2-quality-control |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
0 |
4 |
4 |
6 |
6 |
11 |
11 |
105 |
105 |
4 |
4 |
11 |
11 |
0 |
0 |
0 |
0 |
122 |
122 |
19 |
19 |
|
|
True |
False |
|
qiime2 |
qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac |
qza |
|
2022-08-26 |
https://github.com/qiime2/q2-diversity-lib |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
12 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
0 |
0 |
4 |
4 |
33 |
33 |
8 |
8 |
47 |
47 |
6 |
6 |
2850 |
2850 |
2 |
2 |
3 |
3 |
2933 |
2933 |
20 |
20 |
https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927 |
|
True |
False |
|
qiime2 |
qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask |
qza |
|
2022-08-26 |
https://github.com/qiime2/q2-alignment |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
67 |
67 |
390 |
390 |
35 |
35 |
78 |
78 |
16 |
16 |
114 |
114 |
14 |
14 |
69 |
69 |
651 |
651 |
132 |
132 |
|
|
True |
False |
|
qiime2 |
qiime2__vizard__boxplot, qiime2__vizard__heatmap, qiime2__vizard__lineplot, qiime2__vizard__scatterplot_2d |
qzv |
|
2024-10-30 |
https://github.com/qiime2/q2-vizard |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
20 |
20 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
20 |
20 |
5 |
5 |
|
|
True |
False |
|
qiime2 |
qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap |
qzv, qza |
|
2022-08-26 |
https://github.com/qiime2/q2-diversity |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
21 |
21 |
22 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21 |
0 |
0 |
135 |
135 |
3770 |
3770 |
88 |
88 |
2286 |
2286 |
60 |
60 |
1211 |
1211 |
26 |
26 |
360 |
360 |
7627 |
7627 |
309 |
309 |
https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, https://usegalaxy.org.au/published/workflow?id=543001c51567b438, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=c6b6524108f53688, https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318 |
|
True |
False |
|
qiime2 |
qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts |
qza, qzv |
|
2022-08-26 |
https://github.com/qiime2/q2-demux |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
0 |
289 |
289 |
1358 |
1358 |
251 |
251 |
1071 |
1071 |
91 |
91 |
1146 |
1146 |
28 |
28 |
127 |
127 |
3702 |
3702 |
659 |
659 |
https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, https://usegalaxy.eu/published/workflow?id=ca5da5179cefec8b, https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8, https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e, https://usegalaxy.org.au/published/workflow?id=3c1bf73067334071, https://usegalaxy.org.au/published/workflow?id=57aa23f4f0418a07, https://usegalaxy.org.au/published/workflow?id=cddd668a29b1488a, https://usegalaxy.org.au/published/workflow?id=f946d722f7c27479, https://usegalaxy.org/published/workflow?id=0dc387dc861bdb61, https://usegalaxy.org/published/workflow?id=4ca9319c98be08f8, https://usegalaxy.org/published/workflow?id=685b0de4c31f6695, https://usegalaxy.org/published/workflow?id=76b2c4762dd61d03, https://usegalaxy.org/published/workflow?id=7aa87e7f9cfdae78, https://usegalaxy.org/published/workflow?id=a7cc1038b14f2201, https://usegalaxy.org/published/workflow?id=b335f75495dab9b4, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://workflowhub.eu/workflows/893?version=3 |
|
True |
False |
|
qiime2 |
qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats |
qza, qzv |
|
2022-08-26 |
https://github.com/biocore/deblur |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
40 |
40 |
225 |
225 |
24 |
24 |
78 |
78 |
9 |
9 |
177 |
177 |
1 |
1 |
8 |
8 |
488 |
488 |
74 |
74 |
|
|
True |
False |
|
qiime2 |
qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single, qiime2__dada2__plot_base_transitions |
qza, qzv |
|
2022-08-26 |
http://benjjneb.github.io/dada2/ |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
319 |
319 |
2670 |
2670 |
253 |
253 |
1230 |
1230 |
79 |
79 |
843 |
843 |
29 |
29 |
182 |
182 |
4925 |
4925 |
680 |
680 |
https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3 |
|
True |
False |
|
qiime2 |
qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single |
qza |
|
2022-08-26 |
https://github.com/qiime2/q2-cutadapt |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
73 |
73 |
364 |
364 |
69 |
69 |
273 |
273 |
7 |
7 |
213 |
213 |
3 |
3 |
31 |
31 |
881 |
881 |
152 |
152 |
|
|
True |
False |
|
qiime2 |
qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__ancombc2, qiime2__composition__ancombc2_visualizer, qiime2__composition__da_barplot, qiime2__composition__tabulate |
qza, qzv |
|
2022-08-26 |
https://github.com/qiime2/q2-composition |
2026.1.0+0.g4b3aa86.dirty-q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
26 |
26 |
388 |
388 |
31 |
31 |
256 |
256 |
8 |
8 |
325 |
325 |
9 |
9 |
89 |
89 |
1058 |
1058 |
74 |
74 |
|
|
True |
False |
|
qiime2 |
qiime2__taxa__barplot, qiime2__taxa__barplot2, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table |
qzv, qza |
|
2022-08-26 |
https://github.com/qiime2/q2-taxa |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
266 |
266 |
2747 |
2747 |
159 |
159 |
1008 |
1008 |
78 |
78 |
690 |
690 |
22 |
22 |
236 |
236 |
4681 |
4681 |
525 |
525 |
https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4 |
|
True |
False |
|
qiime2 |
qiime2__boots__alpha, qiime2__boots__alpha_average, qiime2__boots__alpha_collection, qiime2__boots__beta, qiime2__boots__beta_average, qiime2__boots__beta_collection, qiime2__boots__core_metrics, qiime2__boots__kmer_diversity, qiime2__boots__resample |
qza, qzv |
|
2025-11-01 |
https://library.qiime2.org/plugins/caporaso-lab/q2-boots |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__boots |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__boots |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
qiime2 |
qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref |
qza, qzv |
|
2022-08-26 |
https://github.com/qiime2/q2-vsearch |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
8 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
0 |
31 |
31 |
409 |
409 |
18 |
18 |
280 |
280 |
5 |
5 |
24 |
24 |
10 |
10 |
77 |
77 |
790 |
790 |
64 |
64 |
|
|
True |
False |
|
qiime2 |
qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot |
qzv |
|
2022-08-26 |
http://biocore.github.io/emperor/build/html/index.html |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
42 |
42 |
142 |
142 |
34 |
34 |
198 |
198 |
15 |
15 |
195 |
195 |
9 |
9 |
27 |
27 |
562 |
562 |
100 |
100 |
|
|
True |
False |
|
qiime2 |
qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global |
qza |
|
2022-08-26 |
https://github.com/qiime2/q2-feature-classifier |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
10 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
0 |
0 |
325 |
325 |
3046 |
3046 |
232 |
232 |
1256 |
1256 |
88 |
88 |
1282 |
1282 |
28 |
28 |
178 |
178 |
5762 |
5762 |
673 |
673 |
https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927 |
|
True |
False |
|
qiime2 |
qiime2__feature_table___summarize, qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__normalize, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose |
qzv, qza |
|
2022-08-26 |
https://github.com/qiime2/q2-feature-table |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
17 |
17 |
17 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
17 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
17 |
0 |
0 |
298 |
298 |
5335 |
5335 |
203 |
203 |
1938 |
1938 |
95 |
95 |
2932 |
2932 |
28 |
28 |
591 |
591 |
10796 |
10796 |
624 |
624 |
https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3 |
|
True |
False |
|
qiime2 |
qiime2__fondue___get_sequences, qiime2__fondue__combine_seqs, qiime2__fondue__get_all, qiime2__fondue__get_ids_from_query, qiime2__fondue__get_metadata, qiime2__fondue__get_sequences, qiime2__fondue__merge_metadata, qiime2__fondue__scrape_collection |
qza |
|
2025-11-01 |
https://github.com/bokulich-lab/q2-fondue |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fondue |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fondue |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
qiime2 |
qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp |
qza |
|
2022-08-26 |
https://github.com/qiime2/q2-fragment-insertion |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
16 |
16 |
81 |
81 |
7 |
7 |
59 |
59 |
1 |
1 |
6 |
6 |
2 |
2 |
2 |
2 |
148 |
148 |
26 |
26 |
https://usegalaxy.eu/published/workflow?id=6ad6d87618c4e405 |
|
True |
False |
|
qiime2 |
qiime2__kmerizer__core_metrics, qiime2__kmerizer__seqs_to_kmers |
qza, qzv |
|
2025-11-01 |
https://github.com/bokulich-lab/q2-kmerizer |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__kmerizer |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__kmerizer |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
qiime2 |
qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility |
qzv, qza |
|
2022-08-26 |
https://github.com/qiime2/q2-longitudinal |
2026.1.0+q2galaxy.2026.1.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
11 |
11 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
0 |
0 |
12 |
12 |
63 |
63 |
7 |
7 |
60 |
60 |
6 |
6 |
142 |
142 |
2 |
2 |
8 |
8 |
273 |
273 |
27 |
27 |
|
|
True |
False |
|
qiime2_dbotu_q2 |
qiime2_dbotu_q2 |
qza |
q2-dbotu is a Qiime 2 plugin for performing OTU clustering |
2025-03-20 |
https://github.com/cduvallet/q2-dbotu/tree/master |
2022.11.1+galaxy0 |
|
|
To update |
Metagenomics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/qiime2_dbotu_q2/ |
https://github.com/bgruening/galaxytools/tree/master/tools/qiime2_dbotu_q2 |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
13 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
13 |
7 |
7 |
|
|
True |
False |
|
qualifilter |
qualifilter |
tsv, csv, txt |
Extracts and summarizes QC metrics from MultiQC tabular output to produce a clean, threshold-based QC matrix. |
2025-12-15 |
https://github.com/galaxyproject/tools-iuc |
1.0.0 |
qualifilter |
1.0.0 |
Up-to-date |
Sequence Analysis, Statistics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
qualimap |
qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq |
html, tsv |
Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. |
2019-10-10 |
http://qualimap.bioinfo.cipf.es/ |
2.3 |
qualimap |
2.3 |
Up-to-date |
Sequence Analysis, Transcriptomics, SAM |
Sequencing quality control |
Sequencing quality control |
Data quality management |
Data quality management |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap |
qualimap |
QualiMap |
Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. |
|
4 |
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
4 |
4 |
4 |
0 |
2949 |
3172 |
735774 |
740034 |
3586 |
3810 |
117198 |
120922 |
847 |
882 |
36259 |
41650 |
70 |
70 |
6924 |
6924 |
909530 |
896155 |
7934 |
7452 |
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variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon, variant-analysis/tb-variant-analysis |
True |
False |
|
quast |
quast |
tabular, html, pdf, txt, png |
Quast (Quality ASsessment Tool) evaluates genome assemblies. |
2016-09-07 |
http://quast.bioinf.spbau.ru/ |
5.3.0 |
quast |
5.3.0 |
Up-to-date |
Assembly |
Visualisation, Sequence assembly validation |
Visualisation, Sequence assembly validation |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast |
quast |
QUAST |
QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
11028 |
11672 |
120605 |
126603 |
13078 |
14773 |
78457 |
86986 |
4849 |
5353 |
46644 |
50987 |
613 |
619 |
14902 |
14963 |
279539 |
260608 |
32417 |
29568 |
https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=085c227c9a56fcae, https://usegalaxy.eu/published/workflow?id=0ebfab0e957b7267, https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=165089132248a0b0, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=1ea8bfbe6cb04531, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=30b514cfb9cce524, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef, 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https://usegalaxy.org/published/workflow?id=109092d8dbda4398, https://usegalaxy.org/published/workflow?id=1c7af480caf150bd, https://usegalaxy.org/published/workflow?id=3cf46c167ccb374f, https://usegalaxy.org/published/workflow?id=4029a0c8fa23d375, https://usegalaxy.org/published/workflow?id=4161cfd67ed94b5d, https://usegalaxy.org/published/workflow?id=4d1279007d0137fa, https://usegalaxy.org/published/workflow?id=4e1ae78405034ad3, https://usegalaxy.org/published/workflow?id=51c485af11d90700, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb, 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https://workflowhub.eu/workflows/225?version=1, https://workflowhub.eu/workflows/229?version=1, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/750?version=3, https://workflowhub.eu/workflows/794?version=2 |
assembly/assembly-quality-control, assembly/general-introduction, assembly/hifi-assembly, assembly/hybrid_denovo_assembly, assembly/largegenome, assembly/metagenomics-assembly, assembly/mrsa-illumina, assembly/mrsa-nanopore, assembly/unicycler-assembly, assembly/vgp_genome_assembly, assembly/vgp_workflow_training, microbiome/metagenomics-assembly |
True |
False |
|
quickmerge |
quickmerge |
fasta, tabular |
Merge long-read and hybrid assemblies to increase contiguity |
2022-07-08 |
https://github.com/mahulchak/quickmerge |
0.3 |
quickmerge |
0.3 |
Up-to-date |
Assembly |
Genome assembly, Scaffolding, De-novo assembly, Genotyping |
Genome assembly, Scaffolding, De-novo assembly, Genotyping |
Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype |
Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge |
quickmerge |
quickmerge |
Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
quicktree |
quicktree |
newick |
neighbour-joining phylogenetic inference |
2024-11-21 |
https://github.com/khowe/quicktree |
2.5 |
quicktree |
2.5 |
Up-to-date |
Phylogenetics |
Phylogenetic inference (from molecular sequences) |
Phylogenetic inference (from molecular sequences) |
Phylogenetics |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree |
quicktree |
QuickTree |
QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
69 |
69 |
466 |
466 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
466 |
466 |
69 |
69 |
https://workflowhub.eu/workflows/1650?version=1 |
sequence-analysis/tapscan-streptophyte-algae |
True |
False |
|
racon |
racon |
fasta |
Consensus module for raw de novo DNA assembly of long uncorrected reads. |
2018-06-11 |
https://github.com/isovic/racon |
1.5.0 |
racon |
1.5.0 |
Up-to-date |
Sequence Analysis |
Genome assembly, Mapping assembly |
Genome assembly, Mapping assembly |
Whole genome sequencing, Sequence assembly |
Whole genome sequencing, Sequence assembly |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/racon |
https://github.com/bgruening/galaxytools/tree/master/tools/racon |
Racon |
Racon |
Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1046 |
1151 |
32503 |
37525 |
683 |
683 |
23074 |
23074 |
263 |
268 |
9144 |
9214 |
31 |
31 |
320 |
320 |
70133 |
65041 |
2133 |
2023 |
https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a4f50449afde4a05, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=0c421197e022f323, https://usegalaxy.org.au/published/workflow?id=1ff6aabb7e3954ac, https://usegalaxy.org.au/published/workflow?id=45e9910f46a210d8, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=bcdc5ce2ea8700fc, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1599?version=1, https://workflowhub.eu/workflows/1604?version=1, https://workflowhub.eu/workflows/227?version=1, https://workflowhub.eu/workflows/228?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/51?version=1, https://workflowhub.eu/workflows/563?version=1 |
assembly/largegenome, microbiome/plasmid-metagenomics-nanopore |
True |
False |
|
rasusa |
rasusa |
bam |
Randomly subsample sequencing reads to a specified coverage |
2024-02-16 |
https://github.com/mbhall88/rasusa |
2.0.0 |
rasusa |
2.2.2 |
To update |
Sequence Analysis |
Sequence assembly validation, Sequencing quality control |
Sequence assembly validation |
Genomics, Sequence analysis, Sequence assembly, Sequencing, RNA-Seq |
Genomics, Sequence analysis, Sequence assembly, RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa |
rasusa |
rasusa |
Rasusa: Randomly subsample sequencing reads to aspecified coverageProduces an unbiased subsample of your reads |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
24 |
24 |
104 |
104 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
104 |
104 |
24 |
24 |
|
|
True |
False |
|
raxml |
raxml |
txt, nhx |
RAxML - A Maximum Likelihood based phylogenetic inference |
2015-11-05 |
http://www.exelixis-lab.org/web/software/raxml/ |
8.2.12 |
raxml |
8.2.13 |
To update |
Phylogenetics |
Sequence analysis, Phylogenetic tree analysis |
Sequence analysis |
Phylogenetics, Sequence analysis |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml |
raxml |
RAxML |
A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1422 |
1464 |
15492 |
16986 |
1144 |
1144 |
19599 |
19633 |
731 |
1034 |
5870 |
7945 |
21 |
21 |
305 |
305 |
44869 |
41266 |
3663 |
3318 |
https://usegalaxy.eu/published/workflow?id=470656ef317c9dd5, https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://workflowhub.eu/workflows/1577?version=1 |
evolution/mtb_phylogeny |
True |
False |
|
raxmlng |
raxmlng |
txt, nhx |
RAxML-NG - A Maximum Likelihood based phylogenetic tree inference |
2025-12-20 |
http://www.exelixis-lab.org/web/software/raxml-ng/ |
1.2.2 |
raxml-ng |
1.2.2 |
Up-to-date |
Phylogenetics |
Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree bootstrapping |
Phylogenetic tree bootstrapping |
Phylogenetics, Agricultural science, Phylogenomics |
Phylogenetics, Agricultural science, Phylogenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxmlng |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxmlng |
RAxML-NG |
RAxML-NG |
Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
read2tree |
read2tree |
newick |
Infer a species tree from sequencing reads. |
2025-11-23 |
https://github.com/DessimozLab/read2tree |
2.0.1 |
read2tree |
2.0.1 |
Up-to-date |
Phylogenetics |
|
|
Phylogenomics |
Phylogenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/read2tree |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/read2tree |
read2tree |
read2tree |
read2tree is a software tool for generating alignment matrices and performing tree inference directly from sequencing reads. It leverages the OMA database and a set of input reads, bypassing many of the standard steps typically required in phylogenomic analysis. In particular, it avoids for read filtering, assembly, gene prediction, gene annotation, all-vs-all comparison, orthology prediction, alignment, and concatenation. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
read_it_and_keep |
read_it_and_keep |
|
Rapid decontamination of SARS-CoV-2 sequencing reads |
2022-01-28 |
https://github.com/GenomePathogenAnalysisService/read-it-and-keep |
0.2.2 |
read-it-and-keep |
0.3.0 |
To update |
Sequence Analysis |
Filtering, Genome alignment |
Filtering, Genome alignment |
Pathology, Genomics |
Pathology, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep |
read_it_and_keep |
read_it_and_keep |
Read-it-and-keep is a bioinformatics tool designed to filter and extract sequencing reads according to user-defined criteria, such as the presence of specific motifs or coverage of regions of interest. This type of filtering can be particularly useful for targeted analyses, where only relevant sequences are retained for further study, optimising computing and storage resources. |
|
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
81 |
81 |
3781 |
3781 |
8 |
8 |
9 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3790 |
3790 |
89 |
89 |
https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://usegalaxy.eu/published/workflow?id=d967194ca51ff11e, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/521?version=1 |
|
True |
False |
|
reago |
reago |
fasta |
Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. |
2015-12-09 |
https://github.com/chengyuan/reago-1.1 |
1.1 |
reago |
1.1 |
Up-to-date |
Metagenomics, RNA |
Sequence assembly |
Sequence assembly |
Sequence assembly, RNA, Metagenomics, Microbiology |
Sequence assembly, RNA, Metagenomics, Microbiology |
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago |
reago |
REAGO |
This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
18 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
7 |
7 |
|
|
True |
False |
|
recentrifuge |
recentrifuge |
html, txt, tabular, xlsx |
"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." |
2022-05-04 |
https://github.com/khyox/recentrifuge |
1.16.1 |
recentrifuge |
2.0.0 |
To update |
Metagenomics |
Taxonomic classification, Expression analysis, Cross-assembly |
Taxonomic classification, Expression analysis, Cross-assembly |
Metagenomics, Microbial ecology, Metagenomic sequencing |
Metagenomics, Microbial ecology, Metagenomic sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge |
Recentrifuge |
Recentrifuge |
Robust comparative analysis and contamination removal for metagenomics. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
306 |
306 |
2546 |
2546 |
160 |
160 |
593 |
593 |
37 |
37 |
105 |
105 |
27 |
27 |
2397 |
2397 |
5641 |
5641 |
530 |
530 |
https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502, https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88, https://usegalaxy.eu/published/workflow?id=0c47571d20535426, https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=47e14222073e7192, https://usegalaxy.eu/published/workflow?id=884a4415b669690c, https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75, https://usegalaxy.eu/published/workflow?id=bb63b5bb983fd49c, https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264, https://usegalaxy.eu/published/workflow?id=c14d2e8b3c191bc4, https://usegalaxy.eu/published/workflow?id=c930a54a30dcc7e3, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962, https://usegalaxy.eu/published/workflow?id=ebb131f2a6172081, https://usegalaxy.fr/published/workflow?id=3d3b40398d1cd1ae, https://usegalaxy.org/published/workflow?id=1be5c982c2d36a6c, https://usegalaxy.org/published/workflow?id=2a782ad24271f570, https://usegalaxy.org/published/workflow?id=323c651ca583c9e5, https://usegalaxy.org/published/workflow?id=4f698eaeef30e364, https://usegalaxy.org/published/workflow?id=623fc80c7f91a33a, https://usegalaxy.org/published/workflow?id=9f68718f025bed30, https://usegalaxy.org/published/workflow?id=b6a795834009ce06, https://usegalaxy.org/published/workflow?id=de9bf4c1024f8d53, https://usegalaxy.org/published/workflow?id=dfd73857c0eb2a21, https://usegalaxy.org/published/workflow?id=f378960ee55f567e, https://workflowhub.eu/workflows/1052?version=11, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1674?version=2, https://workflowhub.eu/workflows/1881?version=2, https://workflowhub.eu/workflows/1882?version=3, https://workflowhub.eu/workflows/2043?version=1 |
ecology/bacterial-isolate-species-contamination-checking, sequence-analysis/quality-contamination-control |
True |
False |
|
remove_terminal_stop_codons |
remove_terminal_stop_codons |
fasta |
Remove terminal stop codons from coding sequences |
2025-12-04 |
https://github.com/veg/CAPHEINE |
1.0.0 |
biopython |
1.70 |
To update |
Phylogenetics, Sequence Analysis, Fasta Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/remove_terminal_stop_codons |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/remove_terminal_stop_codons |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
repeatexplorer2 |
repeatexplorer_clustering |
html |
Tool for annotation of repeats from unassembled shotgun reads. |
2023-11-01 |
https://github.com/repeatexplorer/repex_tarean |
2.3.8 |
|
|
To update |
Genome annotation |
|
|
|
|
gga |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
83 |
83 |
369 |
369 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
369 |
369 |
83 |
83 |
|
|
True |
False |
|
roary |
roary |
tabular, fasta, csv, nhx, dot, embl, txt |
Roary the pangenome pipeline |
2017-06-21 |
https://sanger-pathogens.github.io/Roary/ |
3.13.0 |
roary |
3.13.0 |
Up-to-date |
Sequence Analysis |
Genome assembly |
Genome assembly |
DNA, Genomics, Mapping |
DNA, Genomics, Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary |
roary |
Roary |
A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
2251 |
2377 |
21218 |
23887 |
2319 |
2454 |
17744 |
18851 |
653 |
749 |
5251 |
7169 |
47 |
47 |
187 |
187 |
50094 |
44400 |
5627 |
5270 |
https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=b1a799497c366eef, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org/published/workflow?id=78d8b738f5715a8a, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb |
|
True |
False |
|
rseqc |
rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin |
tabular, wig, txt, pdf |
an RNA-seq quality control package |
2017-02-27 |
https://code.google.com/p/rseqc/ |
5.0.3 |
rseqc |
5.0.4 |
To update |
Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization |
Data handling |
Data handling |
Sequencing |
Sequencing |
nilesh |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc |
rseqc |
RSeQC |
Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. |
|
22 |
22 |
22 |
22 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
0 |
0 |
0 |
22 |
22 |
22 |
0 |
4113 |
5223 |
155237 |
181534 |
4079 |
5016 |
146353 |
197501 |
629 |
697 |
28108 |
32069 |
809 |
810 |
78294 |
78366 |
489470 |
407992 |
11746 |
9630 |
https://usegalaxy.eu/published/workflow?id=1ee43d90b69829e9, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=5e4135eeb4972709, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=a52c5dd688def9ba, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.eu/published/workflow?id=cc37667c2d1f9056, https://usegalaxy.eu/published/workflow?id=ccef778cfd9024d1, https://usegalaxy.eu/published/workflow?id=f33b5135ee99e0dc, https://usegalaxy.fr/published/workflow?id=334189184455d9a2, https://usegalaxy.fr/published/workflow?id=5d83e0886f2a7465, https://usegalaxy.fr/published/workflow?id=74b4d11c07f7f0a4, https://usegalaxy.fr/published/workflow?id=826cffb2458e4067, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=85aede91db0122e4, https://usegalaxy.org.au/published/workflow?id=a763e53653b10ce0, https://usegalaxy.org.au/published/workflow?id=af7b95f46485308c, https://usegalaxy.org.au/published/workflow?id=b08342866a118a5e, https://usegalaxy.org.au/published/workflow?id=bb0feff5d764df60, https://usegalaxy.org.au/published/workflow?id=ce7f6a1c824920e2, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=044c5ce43f2e1829, https://usegalaxy.org/published/workflow?id=582f3de3971fc38c, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=682b1c7e2ad9d443, https://usegalaxy.org/published/workflow?id=7022c4d9af725e5c, https://usegalaxy.org/published/workflow?id=73f5b1a6fd3c703f, https://usegalaxy.org/published/workflow?id=76b8ed1c68678b62, https://usegalaxy.org/published/workflow?id=7e9269e78e989480, https://usegalaxy.org/published/workflow?id=a743746151101352, https://usegalaxy.org/published/workflow?id=b11796364c22235e, https://usegalaxy.org/published/workflow?id=b1a98a2d5ebda1c5, https://usegalaxy.org/published/workflow?id=e035be74e3c85bf5, https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1675?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1692?version=1, https://workflowhub.eu/workflows/1695?version=1, https://workflowhub.eu/workflows/688?version=1 |
transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts |
True |
False |
|
scoary |
scoary |
tabular, newick |
Scoary calculates the assocations between all genes in the accessory genome and the traits. |
2021-03-18 |
https://github.com/AdmiralenOla/Scoary |
1.6.16 |
scoary |
1.6.16 |
Up-to-date |
Metagenomics |
Analysis |
Analysis |
Genotype and phenotype, Model organisms, GWAS study, Functional genomics |
Genotype and phenotype, Model organisms, GWAS study, Functional genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary |
scoary |
Scoary |
Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
113 |
113 |
1366 |
1366 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1366 |
1366 |
113 |
113 |
|
|
True |
False |
|
semibin |
semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train |
fasta, csv |
SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks |
2022-10-14 |
https://semibin.readthedocs.io/en/latest/ |
2.1.0 |
semibin |
2.2.1 |
To update |
Metagenomics |
Sequence assembly, Read binning |
Sequence assembly, Read binning |
Metagenomics, Machine learning, Microbial ecology, Sequence assembly |
Metagenomics, Machine learning, Microbial ecology, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin |
semibin |
SemiBin |
Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. |
|
1 |
6 |
6 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
6 |
0 |
0 |
53 |
53 |
2779 |
2779 |
9 |
9 |
18 |
18 |
0 |
0 |
0 |
0 |
2 |
2 |
75 |
75 |
2872 |
2872 |
64 |
64 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1 |
microbiome/metagenomics-binning |
True |
False |
|
seqkit |
seqkit_fx2tab, seqkit_grep, seqkit_head, seqkit_locate, seqkit_sort, seqkit_split2, seqkit_stats, seqkit_translate |
tabular, txt |
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation |
2022-06-01 |
https://bioinf.shenwei.me/seqkit/ |
2.12.0 |
seqkit |
2.12.0 |
Up-to-date |
Sequence Analysis |
DNA transcription, Sequence trimming, DNA translation, Sequence conversion |
DNA transcription, Sequence trimming, DNA translation |
Database management, Sequence analysis |
Database management, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit |
seqkit |
seqkit |
FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. |
|
3 |
6 |
7 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
396 |
396 |
13926 |
13926 |
0 |
0 |
0 |
0 |
120 |
120 |
2190 |
2190 |
69 |
69 |
648 |
648 |
16764 |
16764 |
585 |
585 |
https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56, https://workflowhub.eu/workflows/2024?version=2, https://workflowhub.eu/workflows/2036?version=1, https://workflowhub.eu/workflows/2038?version=1, https://workflowhub.eu/workflows/601?version=2, https://workflowhub.eu/workflows/602?version=2, https://workflowhub.eu/workflows/697?version=1 |
|
True |
False |
|
seqprep |
seqprep |
fastq.gz |
Tool for merging paired-end Illumina reads and trimming adapters. |
2024-01-15 |
https://github.com/jstjohn/SeqPrep |
1.3.2 |
seqprep |
1.3.2 |
Up-to-date |
Fastq Manipulation, Sequence Analysis |
Nucleic acid design |
Nucleic acid design |
Genomics, Sequence assembly, Sequencing, Probes and primers |
Genomics, Sequence assembly, Sequencing, Probes and primers |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep |
seqprep |
SeqPrep |
Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
227 |
227 |
3602 |
3602 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3602 |
3602 |
227 |
227 |
|
microbiome/mgnify-amplicon |
True |
False |
|
seqsero2 |
seqsero2 |
tabular, txt |
Salmonella serotype prediction from genome sequencing data |
2023-11-07 |
https://github.com/denglab/SeqSero2 |
1.3.2 |
seqsero2 |
1.3.2 |
Up-to-date |
Sequence Analysis |
Genome indexing, Antimicrobial resistance prediction, Genome alignment |
Genome indexing, Antimicrobial resistance prediction, Genome alignment |
Whole genome sequencing, Sequence assembly, Genomics |
Whole genome sequencing, Sequence assembly, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 |
seqsero2 |
SeqSero2 |
rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode) |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
116 |
116 |
14011 |
14011 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
14013 |
14013 |
118 |
118 |
https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://workflowhub.eu/workflows/407?version=1 |
|
True |
False |
|
shovill |
shovill |
txt, fasta, unsorted.bam, gfa1 |
Faster de novo assembly pipeline based around Spades |
2017-10-24 |
https://github.com/tseemann/shovill |
1.4.2 |
shovill |
1.4.2 |
Up-to-date |
Assembly |
Genome assembly |
Genome assembly |
Genomics, Microbiology, Sequence assembly |
Genomics, Microbiology, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill |
shovill |
shovill |
Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
3269 |
3491 |
70801 |
76107 |
4933 |
5212 |
51724 |
55190 |
1425 |
1669 |
30312 |
35794 |
83 |
83 |
9136 |
9136 |
176227 |
161973 |
10455 |
9710 |
https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=1ea8bfbe6cb04531, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7, https://usegalaxy.eu/published/workflow?id=4216424f032c055f, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9, https://usegalaxy.eu/published/workflow?id=5b893b69a1b6748f, https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a727e22dc0431614, https://usegalaxy.eu/published/workflow?id=b5ffba506152b1a1, https://usegalaxy.eu/published/workflow?id=b90585626a793502, https://usegalaxy.eu/published/workflow?id=b93333efdab316d8, https://usegalaxy.eu/published/workflow?id=ba1fda2318046543, https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=e532d98f4b368666, https://usegalaxy.eu/published/workflow?id=fca458178b3c794a, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=52065a4100b11184, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f, https://usegalaxy.org.au/published/workflow?id=f2541030f6d70b59, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=0e30324072570abb, https://usegalaxy.org/published/workflow?id=109092d8dbda4398, https://usegalaxy.org/published/workflow?id=1c7af480caf150bd, https://usegalaxy.org/published/workflow?id=3cf46c167ccb374f, https://usegalaxy.org/published/workflow?id=4161cfd67ed94b5d, https://usegalaxy.org/published/workflow?id=4d1279007d0137fa, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=8ebc2b1ae24ed884, https://usegalaxy.org/published/workflow?id=9ac1e4efe310b3b3, https://usegalaxy.org/published/workflow?id=9e5c5ddb60a24889, https://usegalaxy.org/published/workflow?id=b76a9ce44ea019f1, https://usegalaxy.org/published/workflow?id=c454c930ccfb0d3f, https://usegalaxy.org/published/workflow?id=d4c790a45978bb9e, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=db08887d7d6dc147, https://usegalaxy.org/published/workflow?id=e2ab3d3219a648a7, https://usegalaxy.org/published/workflow?id=e75bd7d392e65209, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/102?version=1, https://workflowhub.eu/workflows/103?version=1, https://workflowhub.eu/workflows/1043?version=12, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1602?version=2, https://workflowhub.eu/workflows/1767?version=1, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 |
assembly/mrsa-illumina |
True |
False |
|
sistr_cmd |
sistr_cmd |
csv, json, tabular, fasta |
SISTR in silico serotyping tool |
2017-02-20 |
https://github.com/phac-nml/sistr_cmd |
1.1.3 |
sistr_cmd |
1.1.3 |
Up-to-date |
Sequence Analysis |
Genome assembly, Visualisation, Multilocus sequence typing |
Genome assembly, Visualisation, Multilocus sequence typing |
Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology |
Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology |
nml |
https://github.com/phac-nml/sistr_cmd |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd |
SISTR |
SISTR |
The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
395 |
397 |
5345 |
5466 |
0 |
0 |
0 |
0 |
91 |
95 |
907 |
1010 |
0 |
0 |
0 |
0 |
6476 |
6252 |
492 |
486 |
https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://workflowhub.eu/workflows/407?version=1 |
|
True |
False |
|
smallgenomeutilities |
smgu_frameshift_deletions_checks |
tabular |
Set of utilities for manipulating small viral genome data. |
2023-05-30 |
https://github.com/cbg-ethz/smallgenomeutilities |
0.5.2 |
smallgenomeutilities |
0.5.2 |
Up-to-date |
Sequence Analysis |
Read pre-processing, Sequence alignment, Genetic variation analysis |
Read pre-processing, Sequence alignment, Genetic variation analysis |
Genomics, Population genetics, Workflows, Virology, Sequencing |
Genomics, Population genetics, Workflows, Virology, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities |
v-pipe |
V-pipe |
Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
15 |
15 |
168 |
168 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
168 |
168 |
15 |
15 |
|
|
True |
False |
|
smalt |
smalt |
cigar |
SMALT aligns DNA sequencing reads with a reference genome. |
2017-09-19 |
http://www.sanger.ac.uk/science/tools/smalt-0 |
0.7.6 |
smalt |
0.7.6 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://sourceforge.net/projects/smalt/ |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
snap |
snap, snap_training |
gff, fasta, snaphmm |
SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. |
2017-10-12 |
https://github.com/KorfLab/SNAP |
2013_11_29 |
snap |
2013_11_29 |
Up-to-date |
Sequence Analysis |
Gene prediction |
Gene prediction |
DNA, DNA polymorphism, Genetics |
DNA polymorphism, Genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap |
snap |
SNAP |
The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. |
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
348 |
410 |
1443 |
1821 |
258 |
292 |
813 |
939 |
100 |
101 |
578 |
594 |
0 |
0 |
0 |
0 |
3354 |
2834 |
803 |
706 |
https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://workflowhub.eu/workflows/1504?version=1 |
genome-annotation/annotation-with-maker |
True |
False |
|
snippy |
snippy_core, snippy, snippy_clean_full_aln |
fasta, tabular, txt, vcf, gff3, bam, zip |
Contains the snippy tool for characterising microbial snps |
2017-07-13 |
https://github.com/tseemann/snippy |
|
snippy |
4.6.0 |
To update |
Sequence Analysis |
Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling |
Phylogenetic tree visualisation, Variant calling |
Genomics, Model organisms, DNA polymorphism, Phylogenetics |
Genomics, Model organisms, DNA polymorphism, Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy |
snippy |
snippy |
Rapid haploid variant calling and core SNP phylogeny generation. |
|
3 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
0 |
3483 |
3838 |
188403 |
199916 |
4057 |
4306 |
138187 |
142349 |
2223 |
2852 |
67168 |
78979 |
60 |
60 |
8769 |
8769 |
430013 |
402527 |
11056 |
9823 |
https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=464b642261ed7452, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=65249196143d7930, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=920aab45ff028ed4, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a183da6b56cd1d60, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=d92f9c33dded693f, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=1719e0eb54b41f68, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=5674956f5c18b85b, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://usegalaxy.org/published/workflow?id=ee4679b3e9e830b7, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1573?version=1, https://workflowhub.eu/workflows/1639?version=1, https://workflowhub.eu/workflows/1647?version=2, https://workflowhub.eu/workflows/2049?version=1 |
evolution/mtb_transmission, variant-analysis/microbial-variants, variant-analysis/tb-variant-analysis |
True |
False |
|
sonneityping |
sonneityping |
tabular |
Scripts for parsing Mykrobe predict results for Shigella sonnei. |
2021-09-16 |
https://github.com/katholt/sonneityping |
20210201 |
sonneityping |
20210201 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction, Variant calling, Genotyping |
Antimicrobial resistance prediction, Variant calling, Genotyping |
Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics |
Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping |
sonneityping |
sonneityping |
Scripts for parsing Mykrobe predict results for Shigella sonnei. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
|
|
True |
False |
|
sortmerna |
bg_sortmerna |
bam, tabular, txt |
SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. |
2015-02-28 |
http://bioinfo.lifl.fr/RNA/sortmerna/ |
4.3.6 |
sortmerna |
4.3.7 |
To update |
RNA |
Sequence similarity search, Sequence comparison, Sequence alignment analysis |
Sequence similarity search, Sequence alignment analysis |
Metatranscriptomics, Metagenomics |
Metatranscriptomics, Metagenomics |
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna |
sortmerna |
SortMeRNA |
Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1135 |
1352 |
23920 |
26406 |
581 |
581 |
6479 |
6479 |
219 |
225 |
3668 |
3882 |
116 |
116 |
648 |
651 |
37418 |
34715 |
2274 |
2051 |
https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.eu/published/workflow?id=f6e8a63283262518, https://usegalaxy.eu/published/workflow?id=fd90652d475ed739, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.fr/published/workflow?id=e6991d64e851b09e, https://usegalaxy.org.au/published/workflow?id=408a31694e9c85e6, https://workflowhub.eu/workflows/1444?version=2, https://workflowhub.eu/workflows/1466?version=2 |
microbiome/metatranscriptomics, microbiome/metatranscriptomics-short |
True |
False |
|
spades |
spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades |
fasta, txt |
SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. |
2016-12-21 |
https://github.com/ablab/spades |
4.2.0 |
spades |
4.2.0 |
Up-to-date |
Assembly, RNA, Metagenomics |
Genome assembly |
Genome assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades |
spades |
SPAdes |
St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. |
|
9 |
9 |
9 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
3 |
9 |
3 |
0 |
8250 |
8882 |
104429 |
116176 |
14023 |
14731 |
147425 |
154112 |
5211 |
6722 |
62902 |
76811 |
373 |
380 |
2677 |
2762 |
349861 |
317433 |
30715 |
27857 |
https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09, https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://usegalaxy.eu/published/workflow?id=7b755497d168cb13, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=a6b0234c6393b85e, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=a847773b563b2328, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=c702c76cadebac30, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=db10c092fad70d69, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.fr/published/workflow?id=5bb882218afda132, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=38d992baf9a2a2bc, https://usegalaxy.org.au/published/workflow?id=39c724282ee008e3, https://usegalaxy.org.au/published/workflow?id=813a4938397cf6ee, https://usegalaxy.org.au/published/workflow?id=87cdeb05b1ebeab0, https://usegalaxy.org.au/published/workflow?id=8abcfe166f1a6cd8, https://usegalaxy.org.au/published/workflow?id=8f7d5ebead46a6d0, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=15cca0e249f40aea, https://usegalaxy.org/published/workflow?id=18899840e49d89c3, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=5039ae2c81d0aba8, https://usegalaxy.org/published/workflow?id=71f8a4090877f171, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=87b3305ea433b4e2, https://usegalaxy.org/published/workflow?id=8a350e0d96e937a5, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://usegalaxy.org/published/workflow?id=9ba6da7dae465d3e, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=ae81cc0e8263d03e, https://usegalaxy.org/published/workflow?id=d3357032209bbd02, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1626?version=1, https://workflowhub.eu/workflows/1634?version=1, https://workflowhub.eu/workflows/2046?version=1, https://workflowhub.eu/workflows/2047?version=1, https://workflowhub.eu/workflows/2048?version=1, https://workflowhub.eu/workflows/434?version=1, https://workflowhub.eu/workflows/52?version=1, https://workflowhub.eu/workflows/68?version=1 |
assembly/debruijn-graph-assembly, assembly/metagenomics-assembly, microbiome/metagenomics-assembly |
True |
False |
|
spotyping |
spotyping |
txt, excel.xls, pdf |
SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads |
2018-05-07 |
https://github.com/xiaeryu/SpoTyping-v2.0 |
2.1 |
spotyping |
2.1 |
Up-to-date |
Sequence Analysis |
Variant pattern analysis |
Variant pattern analysis |
Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation |
Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping |
spotyping |
SpoTyping |
Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
34 |
34 |
2042 |
2042 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2042 |
2042 |
34 |
34 |
|
|
True |
False |
|
squirrel |
squirrel_phylo, squirrel_qc |
nexus, fasta, svg, png, csv |
QC and Phylogenetic analysis of MPXV |
2025-01-16 |
https://github.com/aineniamh/squirrel |
1.0.13 |
squirrel |
1.3.2 |
To update |
Phylogenetics |
Phylogenetic analysis, Sequencing quality control |
Phylogenetic analysis, Sequencing quality control |
Virology |
Virology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel |
squirrel |
squirrel |
Some QUIck Reconstruction to Resolve Evolutionary LinksSquirrel provides a rapid way of producing reliable alignments for MPXV and also enable maximum-likelihood phylogenetics pipeline tree estimation. |
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
7 |
7 |
0 |
0 |
0 |
0 |
41 |
41 |
193 |
193 |
0 |
0 |
0 |
0 |
200 |
200 |
43 |
43 |
https://usegalaxy.org.au/published/workflow?id=b9fd488b0938d323 |
|
True |
False |
|
sr_bowtie |
bowtieForSmallRNA |
tabular |
bowtie wrapper tool to align small RNA sequencing reads |
2017-09-02 |
http://artbio.fr |
2.3.1 |
bowtie |
1.3.1 |
To update |
RNA, Next Gen Mappers |
|
|
Microbiology, Biology |
Microbiology |
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie |
https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie |
sr_bowtie |
sr_bowtie |
Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25... _Bowtie: http://bowtie-bio.sourceforge.net/index.shtmlA generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.However, this Bowtie wrapper tool only takes FASTQ files as inputs.The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
98 |
98 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
98 |
98 |
2 |
2 |
|
|
True |
False |
|
srst2 |
srst2 |
tabular, fasta |
SRST2 Short Read Sequence Typing for Bacterial Pathogens |
2022-08-22 |
http://katholt.github.io/srst2/ |
0.2.0 |
samtools |
1.23 |
To update |
Metagenomics |
Multilocus sequence typing |
Multilocus sequence typing |
Whole genome sequencing, Public health and epidemiology, Comparative genomics |
Whole genome sequencing, Public health and epidemiology, Comparative genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 |
srst2 |
srst2 |
Short Read Sequence Typing for Bacterial Pathogens |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
68 |
68 |
407 |
407 |
1 |
1 |
71 |
71 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
478 |
478 |
69 |
69 |
https://workflowhub.eu/workflows/407?version=1 |
|
True |
False |
|
srst2 |
srst2 |
bam, tabular, fasta |
Short Read Sequence Typing for Bacterial Pathogens |
2015-12-02 |
|
0.3.7 |
srst2 |
0.2.0 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
68 |
68 |
407 |
407 |
1 |
1 |
71 |
71 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
478 |
478 |
69 |
69 |
https://workflowhub.eu/workflows/407?version=1 |
|
True |
False |
|
staramr |
staramr_search |
tabular, txt, xlsx |
Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. |
2024-09-19 |
https://github.com/phac-nml/staramr |
0.11.1 |
staramr |
0.11.1 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Microbiology, Public health and epidemiology, Infectious disease |
Microbiology, Public health and epidemiology, Infectious disease |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr |
staramr |
staramr |
staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
2921 |
3072 |
31443 |
33124 |
2130 |
2130 |
14763 |
14763 |
1173 |
1182 |
8989 |
9237 |
97 |
97 |
9838 |
9838 |
66962 |
65033 |
6481 |
6321 |
https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=46b6812817c57a01, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=f8fab0cd6fc30d92, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=9, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1488?version=2, https://workflowhub.eu/workflows/2024?version=2, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/470?version=1 |
genome-annotation/amr-gene-detection, microbiome/plasmid-metagenomics-nanopore |
True |
False |
|
stringmlst |
stringmlst |
tabular, txt, fastqsanger |
Rapid and accurate identification of the sequence type (ST) |
2016-10-19 |
|
1.1.0 |
stringMLST |
0.6.3 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
structure |
structure |
txt |
for using multi-locus genotype data to investigate population structure. |
2017-09-22 |
https://web.stanford.edu/group/pritchardlab/structure.html |
2.3.4 |
structure |
2.3.4 |
Up-to-date |
Phylogenetics, Variant Analysis |
Genetic variation analysis |
Genetic variation analysis |
Population genetics |
Population genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure |
structure |
Structure |
The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
138 |
155 |
3903 |
4354 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
330 |
330 |
4684 |
4233 |
158 |
141 |
|
|
True |
False |
|
suite_qiime2_core |
|
|
|
2022-08-29 |
|
|
|
|
To update |
Statistics, Sequence Analysis, Metagenomics |
|
|
|
|
q2d2 |
|
https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
sylph |
sylph_profile, sylph_query |
tabular |
sylph - fast and precise species-level metagenomic profiling with ANIs |
2024-10-08 |
https://github.com/bluenote-1577/sylph |
0.8.1 |
sylph |
0.9.0 |
To update |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Metagenomics |
Metagenomics |
bgruening |
https://github.com/bgruening/galaxytools/main/tools/sylph |
https://github.com/bgruening/galaxytools/tree/master/tools/sylph |
sylph |
sylph |
fast and precise species-level metagenomic profiling with ANIs |
|
2 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
9 |
9 |
257 |
257 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
1 |
1 |
12 |
12 |
270 |
270 |
11 |
11 |
https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://workflowhub.eu/workflows/2068?version=1 |
|
True |
False |
|
syri |
syri |
tabular, vcf |
Synteny and Rearrangement Identifier |
2025-04-16 |
https://github.com/schneebergerlab/syri |
1.7.1 |
syri |
1.7.1 |
Up-to-date |
Sequence Analysis |
Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping |
Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping |
DNA polymorphism, Sequence assembly, DNA structural variation, Mapping, Sequencing |
DNA polymorphism, Sequence assembly, Mapping, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri |
SyRI |
SyRI |
SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies.Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
22 |
84 |
84 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
76 |
76 |
160 |
160 |
27 |
27 |
https://usegalaxy.fr/published/workflow?id=356dced9687596b7, https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef |
|
True |
False |
|
t2ps |
Draw_phylogram |
pdf |
Draw phylogeny |
2014-01-27 |
https://bitbucket.org/natefoo/taxonomy |
1.0.0 |
taxonomy |
0.10.2 |
To update |
Metagenomics |
Phylogenetic tree visualisation |
Phylogenetic tree visualisation |
Phylogenomics |
Phylogenomics |
devteam |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps |
t2ps |
Draw phylogeny |
"Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format." - Galaxy tool wrapper |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
64 |
93 |
405 |
479 |
13 |
1240 |
102 |
7952 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8431 |
507 |
1333 |
77 |
https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c |
|
True |
False |
|
t2t_report |
t2t_report |
tabular |
Summarize taxonomy |
2014-01-27 |
https://bitbucket.org/natefoo/taxonomy |
1.0.0 |
taxonomy |
0.10.2 |
To update |
Metagenomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
55 |
82 |
745 |
1071 |
16 |
1143 |
118 |
7194 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8265 |
863 |
1225 |
71 |
https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c |
|
True |
False |
|
t_coffee |
t_coffee |
clustal, nhx, fasta, msf, phylip, pir, txt, html |
T-Coffee |
2016-12-13 |
https://tcoffee.org/ |
13.45.0.4846264 |
t-coffee |
13.46.0.919e8c6b |
To update |
Sequence Analysis |
|
|
|
|
earlhaminst |
https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/t_coffee |
https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/t_coffee |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
274 |
311 |
3958 |
9664 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9665 |
3959 |
312 |
275 |
https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09 |
|
True |
False |
|
taxonkit |
name2taxid, profile2cami |
tabular, tsv |
TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit |
2024-07-26 |
https://bioinf.shenwei.me/taxonkit/ |
0.20.0 |
taxonkit |
0.20.0 |
Up-to-date |
Metagenomics |
Formatting, Data retrieval |
Formatting, Data retrieval |
Taxonomy, Biotechnology, Ecology |
Taxonomy, Biotechnology, Ecology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit |
taxonkit |
TaxonKit |
TaxonKit is a practical and efficient NCBI taxonomy toolkit. |
|
1 |
1 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
1094 |
1094 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1094 |
1094 |
12 |
12 |
https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1 |
|
True |
False |
|
taxonomy_krona_chart |
taxonomy_krona_chart |
html |
Krona pie chart from taxonomic profile |
2015-08-06 |
http://sourceforge.net/projects/krona/ |
2.7.1+galaxy0 |
krona |
2.8.1 |
To update |
Assembly |
Visualisation |
Visualisation |
Metagenomics |
Metagenomics |
crs4 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart |
krona |
Krona |
Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
7406 |
7874 |
48617 |
51653 |
6438 |
7659 |
33268 |
41191 |
2005 |
2042 |
11003 |
11192 |
162 |
163 |
565 |
586 |
104622 |
93453 |
17738 |
16011 |
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microbiome/beer-data-analysis, microbiome/general-tutorial, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/mgnify-amplicon, microbiome/mothur-miseq-sop, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling |
True |
False |
|
taxpasta |
taxpasta |
tabular, biom1 |
standardise taxonomic profiles |
2023-08-30 |
https://taxpasta.readthedocs.io/en/latest/ |
0.7.0 |
taxpasta |
0.7.0 |
Up-to-date |
Sequence Analysis |
Standardisation and normalisation, Aggregation, Formatting, Conversion |
Standardisation and normalisation, Aggregation, Formatting, Conversion |
Taxonomy, Metagenomics |
Taxonomy, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta |
taxpasta |
taxpasta |
TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
51 |
51 |
323 |
323 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
18 |
18 |
341 |
341 |
52 |
52 |
https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 |
|
True |
False |
|
tb-profiler |
tb_profiler_collate, tb_profiler_profile |
tabular, csv, txt, json, vcf, bam, pdf |
Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. |
2019-04-02 |
https://github.com/jodyphelan/TBProfiler |
6.6.5 |
tb-profiler |
6.6.6 |
To update |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler |
tb-profiler |
tb-profiler |
A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). |
|
1 |
2 |
2 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
491 |
535 |
15947 |
16201 |
490 |
506 |
11483 |
11641 |
199 |
201 |
10939 |
10981 |
0 |
0 |
0 |
0 |
38823 |
38369 |
1242 |
1180 |
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evolution/mtb_transmission, variant-analysis/tb-variant-analysis |
True |
False |
|
tiara |
tiara |
|
Tool for identification of eukaryotic sequences in the metagenomic datasets. |
2024-05-23 |
https://github.com/ibe-uw/tiara |
1.0.3 |
tiara |
|
To update |
Metagenomics, Sequence Analysis |
Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection |
Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection |
Sequencing, Genomics, DNA polymorphism, DNA structural variation |
Sequencing, Genomics, DNA polymorphism |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/tiara |
https://github.com/bgruening/galaxytools/tree/master/tools/tiara |
Tiara |
TIARA |
Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
33 |
33 |
365 |
365 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
365 |
365 |
33 |
33 |
|
|
True |
False |
|
tooldistillator |
tooldistillator, tooldistillator_summarize |
txt, json |
ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files |
2024-04-30 |
https://gitlab.com/ifb-elixirfr/abromics/tooldistillator |
1.0.5 |
tooldistillator |
1.0.5 |
Up-to-date |
Sequence Analysis |
Data parsing |
|
Microbiology, Bioinformatics, Sequence analysis |
Microbiology, Bioinformatics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator |
tooldistillator |
ToolDistillator |
ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. |
|
2 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
121 |
121 |
5042 |
5042 |
162 |
162 |
1550 |
1550 |
0 |
0 |
0 |
0 |
9 |
9 |
19253 |
19253 |
25845 |
25845 |
292 |
292 |
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|
True |
False |
|
transtermhp |
transtermhp |
gff3 |
Finds rho-independent transcription terminators in bacterial genomes |
2015-10-08 |
https://transterm.cbcb.umd.edu |
|
transtermhp |
2.09 |
To update |
Sequence Analysis |
Transcriptional regulatory element prediction |
Transcriptional regulatory element prediction |
Transcription factors and regulatory sites |
Transcription factors and regulatory sites |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp |
transtermhp |
TransTermHP |
TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator |
|
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
59 |
62 |
467 |
502 |
49 |
55 |
170 |
216 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
718 |
637 |
117 |
108 |
|
|
True |
False |
|
treebest_best |
treebest_best |
nhx |
TreeBeST best |
2015-08-06 |
https://treesoft.sourceforge.net/treebest.shtml |
1.9.2.post0 |
treebest |
1.9.2.post1 |
To update |
Phylogenetics |
Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) |
Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) |
Phylogenetics |
Phylogenetics |
earlhaminst |
https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/TreeBest |
https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/TreeBest |
treebest |
TreeBeST |
TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
45 |
58 |
966 |
1033 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1034 |
967 |
59 |
46 |
https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09 |
|
True |
False |
|
trim_galore |
trim_galore |
txt |
Trim Galore adaptive quality and adapter trimmer |
2015-02-28 |
http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
0.6.10 |
trim-galore |
0.6.10 |
Up-to-date |
Sequence Analysis, Fastq Manipulation |
Sequence trimming, Primer removal, Read pre-processing |
Sequence trimming, Primer removal, Read pre-processing |
Sequence analysis |
Sequence analysis |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore |
https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore |
trim_galore |
Trim Galore |
A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
6966 |
8378 |
297289 |
379413 |
13276 |
20041 |
284172 |
418931 |
1722 |
2020 |
36616 |
41727 |
303 |
305 |
3334 |
3366 |
843437 |
621411 |
30744 |
22267 |
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https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=b3026f28a45626a5, https://usegalaxy.org/published/workflow?id=b3823d276917baf0, https://usegalaxy.org/published/workflow?id=bb9e69ae66c3d916, https://usegalaxy.org/published/workflow?id=c4cde7e8d897cd25, https://usegalaxy.org/published/workflow?id=cd56ed91856fcc6f, https://usegalaxy.org/published/workflow?id=d3357032209bbd02, https://usegalaxy.org/published/workflow?id=d5514e327878b531, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=dec0cf06fa059e65, https://usegalaxy.org/published/workflow?id=e04f443a8ceca0d2, https://usegalaxy.org/published/workflow?id=e215018e24b84197, https://usegalaxy.org/published/workflow?id=e26fabceece3b858, https://usegalaxy.org/published/workflow?id=eb33df15225b8aa0, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=ecb279a9114140ab, https://usegalaxy.org/published/workflow?id=eed1aadf2fb83f6c, https://usegalaxy.org/published/workflow?id=eedbd4e9caca6195, https://usegalaxy.org/published/workflow?id=efb62e8178ecdcaf, https://usegalaxy.org/published/workflow?id=f1a9667c0b0999f4, https://usegalaxy.org/published/workflow?id=fcd98ca3abcf6c61, https://workflowhub.eu/workflows/1562?version=1, https://workflowhub.eu/workflows/1615?version=2, https://workflowhub.eu/workflows/1619?version=1, https://workflowhub.eu/workflows/1628?version=1, https://workflowhub.eu/workflows/1657?version=1, https://workflowhub.eu/workflows/1661?version=2, https://workflowhub.eu/workflows/1673?version=1, https://workflowhub.eu/workflows/1717?version=2, https://workflowhub.eu/workflows/99?version=1 |
epigenetics/cut_and_run, epigenetics/estrogen-receptor-binding-site-identification, epigenetics/formation_of_super-structures_on_xi, sequence-analysis/mapping, transcriptomics/mirna-target-finder, transcriptomics/srna, variant-analysis/baculovirus-isolate-variation |
True |
False |
|
trycycler |
trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample |
phylip, newick, fasta |
Trycycler toolkit wrappers |
2021-02-11 |
https://github.com/rrwick/Trycycler |
0.5.5 |
trycycler |
0.5.6 |
To update |
Assembly |
Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation |
Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation |
Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics |
Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler |
trycycler |
Trycycler |
Trycycler: consensus long-read assemblies for bacterial genomes |
|
0 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
0 |
122 |
122 |
15743 |
15743 |
0 |
0 |
0 |
0 |
57 |
57 |
6233 |
6233 |
3 |
3 |
27 |
27 |
22003 |
22003 |
182 |
182 |
|
|
True |
False |
|
tsebra |
tsebra |
gtf, txt |
This tool has been developed to combine BRAKER predictions. |
2023-10-19 |
https://github.com/Gaius-Augustus/TSEBRA |
1.1.2.5 |
tsebra |
1.1.2.5 |
Up-to-date |
Genome annotation |
Homology-based gene prediction, Alternative splicing prediction |
Homology-based gene prediction, Alternative splicing prediction |
Gene expression, RNA-Seq, Gene transcripts, Model organisms |
Gene expression, RNA-Seq, Gene transcripts, Model organisms |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra |
tsebra |
TSEBRA |
TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
51 |
51 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
51 |
51 |
16 |
16 |
|
|
True |
False |
|
unicycler |
unicycler |
gfa1, fasta, bam |
Unicycler is a hybrid assembly pipeline for bacterial genomes. |
2017-05-08 |
https://github.com/rrwick/Unicycler |
0.5.1 |
unicycler |
0.5.1 |
Up-to-date |
Assembly |
Genome assembly, Aggregation |
Genome assembly, Aggregation |
Microbiology, Genomics, Sequencing, Sequence assembly |
Microbiology, Genomics, Sequencing, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler |
unicycler |
Unicycler |
A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
4697 |
5202 |
83521 |
96874 |
5770 |
8769 |
65067 |
104850 |
2392 |
2613 |
22717 |
26831 |
272 |
276 |
2160 |
2183 |
230738 |
173465 |
16860 |
13131 |
https://usegalaxy.eu/published/workflow?id=165089132248a0b0, https://usegalaxy.eu/published/workflow?id=1ea8bfbe6cb04531, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=346b46e6316c6950, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=69be516a48761365, https://usegalaxy.eu/published/workflow?id=7b755497d168cb13, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=8b8e89b9b8801f2f, https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b2dfa74f55a73409, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=c702c76cadebac30, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e8eb80ee09159bac, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=fe43cf59e48bf556, https://usegalaxy.fr/published/workflow?id=5bb882218afda132, https://usegalaxy.org.au/published/workflow?id=38d992baf9a2a2bc, https://usegalaxy.org.au/published/workflow?id=8a40059343cf4b87, https://usegalaxy.org.au/published/workflow?id=8f7d5ebead46a6d0, https://usegalaxy.org.au/published/workflow?id=9c60b83feaa22415, https://usegalaxy.org.au/published/workflow?id=b59fada651043735, https://usegalaxy.org.au/published/workflow?id=b7aa22291322e505, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org.au/published/workflow?id=f01be6a7685ac476, https://usegalaxy.org.au/published/workflow?id=fc3c83b11f527977, https://usegalaxy.org/published/workflow?id=5039ae2c81d0aba8, https://usegalaxy.org/published/workflow?id=69514a75e4c9af08, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=a67afbea4b2eb26b, https://usegalaxy.org/published/workflow?id=b43b72dcf5f7694d, https://usegalaxy.org/published/workflow?id=bc72dcbca89ca35d, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=db0671862a57968d, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1598?version=1, https://workflowhub.eu/workflows/1612?version=1, https://workflowhub.eu/workflows/1616?version=1, https://workflowhub.eu/workflows/2011?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/52?version=1, https://workflowhub.eu/workflows/68?version=1 |
assembly/assembly-with-preprocessing, assembly/hybrid_denovo_assembly, assembly/unicycler-assembly, microbiome/plasmid-metagenomics-nanopore |
True |
False |
|
unipept |
unipept |
d3_hierarchy, tabular, csv |
Unipept retrieves metaproteomics information |
2015-04-03 |
https://github.com/galaxyproteomics/tools-galaxyp |
6.2.4+galaxy1 |
python |
|
To update |
Proteomics |
Prediction and recognition, Visualisation |
Prediction and recognition, Visualisation |
Proteomics, Proteogenomics, Biodiversity, Workflows |
Proteomics, Proteogenomics, Biodiversity, Workflows |
galaxyp |
https://unipept.ugent.be/apidocs |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept |
unipept |
Unipept |
Metaproteomics data analysis with a focus on interactive data visualizations. |
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
282 |
314 |
4723 |
6047 |
102 |
102 |
384 |
384 |
33 |
33 |
1383 |
1383 |
1 |
1 |
1 |
1 |
7815 |
6491 |
450 |
418 |
https://usegalaxy.eu/published/workflow?id=00e246ea459b0991, https://usegalaxy.eu/published/workflow?id=02700454f57eb556, https://usegalaxy.eu/published/workflow?id=0e0be913c3e27022, https://usegalaxy.eu/published/workflow?id=1706bfa819bbfa89, https://usegalaxy.eu/published/workflow?id=17a1433d0b681d4a, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=28af61ead68e0976, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=50d85103f2275d38, https://usegalaxy.eu/published/workflow?id=58db3e1996a8f093, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6766bed39f614b7c, https://usegalaxy.eu/published/workflow?id=68967c922de149ae, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6da171871d4f3fd5, https://usegalaxy.eu/published/workflow?id=755ede37d94dc456, https://usegalaxy.eu/published/workflow?id=78e1769f1dcb797b, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=8f3cafa3bc59ff82, https://usegalaxy.eu/published/workflow?id=8fc1ea9e94bc723d, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=a4d6b9dc6b396933, https://usegalaxy.eu/published/workflow?id=a657b412b37b971b, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=bfe26679d670bb5e, https://usegalaxy.eu/published/workflow?id=c6b6ba35e5b6500a, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=d148459a4d4b91f1, https://usegalaxy.eu/published/workflow?id=d9e7a940b2d410bc, https://usegalaxy.eu/published/workflow?id=df926c5ab8d27192, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://usegalaxy.org.au/published/workflow?id=050a66ff6d4c2b53, https://usegalaxy.org.au/published/workflow?id=f9f685d6150e48c5, https://usegalaxy.org/published/workflow?id=3f797bfb67130883, https://workflowhub.eu/workflows/1219?version=1, https://workflowhub.eu/workflows/1433?version=1, https://workflowhub.eu/workflows/1443?version=1, https://workflowhub.eu/workflows/1450?version=1, https://workflowhub.eu/workflows/1482?version=1 |
microbiome/clinical-mp-5-data-interpretation, proteomics/clinical-mp-5-data-interpretation, proteomics/metaproteomics, proteomics/metaquantome-data-creation |
True |
False |
|
uniprotxml_downloader |
uniprotxml_downloader |
uniprotxml |
Download UniProt proteome in XML or fasta format |
2016-03-08 |
https://www.uniprot.org/help/programmatic_access |
2.5.0 |
requests |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader |
|
|
|
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
239 |
313 |
1805 |
2133 |
73 |
73 |
143 |
143 |
41 |
41 |
1139 |
1139 |
0 |
0 |
0 |
0 |
3415 |
3087 |
427 |
353 |
https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=5374daf356516a40, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=73dc2384535bf6af, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=cb9a26ea53ce7a27, https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d, https://usegalaxy.eu/published/workflow?id=eeb6cff210cac091, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1425?version=1, https://workflowhub.eu/workflows/1464?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 |
microbiome/clinical-mp-1-database-generation, microbiome/clinical-mp-3-verification, proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-3-verification |
True |
False |
|
usher |
usher_matutils, usher_ripples, usher |
txt, tabular, vcf, protobuf3, json, newick |
UShER toolkit wrappers |
2021-05-11 |
https://github.com/yatisht/usher |
0.6.6 |
usher |
0.6.6 |
Up-to-date |
Phylogenetics |
Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) |
Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) |
Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics |
Cladistics, Genotype and phenotype, Phylogenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher |
usher |
usher |
The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
5 |
5 |
1060 |
1060 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1060 |
1060 |
5 |
5 |
|
|
True |
False |
|
valet |
valet |
pdf |
A pipeline for detecting mis-assemblies in metagenomic assemblies. |
2017-11-16 |
https://github.com/marbl/VALET |
|
valet |
1.0 |
To update |
Metagenomics |
Sequence assembly, Sequence assembly visualisation |
Sequence assembly, Sequence assembly visualisation |
Metagenomics, Sequence assembly |
Metagenomics, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet |
valet |
VALET |
VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. |
|
1 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
74 |
101 |
449 |
711 |
67 |
76 |
160 |
249 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
960 |
609 |
177 |
141 |
https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09 |
|
True |
False |
|
vapor |
vapor |
tabular, fasta |
Classify Influenza samples from raw short read sequence data |
2022-08-24 |
https://github.com/wm75/vaporup |
1.0.3 |
vapor |
1.0.3 |
Up-to-date |
Sequence Analysis |
Data retrieval, De-novo assembly, Read mapping |
Data retrieval, De-novo assembly, Read mapping |
Whole genome sequencing, Mapping, Sequence assembly |
Whole genome sequencing, Mapping, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor |
vapor |
VAPOR |
VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. |
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
188 |
188 |
197466 |
197466 |
127 |
127 |
1849 |
1849 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
199315 |
199315 |
315 |
315 |
https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://workflowhub.eu/workflows/1260?version=2 |
variant-analysis/aiv-analysis |
True |
False |
|
varvamp |
varvamp |
txt, fasta, bed, tabular, pdf |
Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses |
2024-01-27 |
https://github.com/jonas-fuchs/varVAMP/ |
1.3 |
varvamp |
1.3 |
Up-to-date |
Sequence Analysis |
PCR primer design |
PCR primer design |
Virology, Probes and primers |
Virology, Probes and primers |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp |
varvamp |
varVAMP |
variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
55 |
55 |
912 |
912 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
912 |
912 |
55 |
55 |
https://workflowhub.eu/workflows/1627?version=1 |
sequence-analysis/viral_primer_design |
True |
False |
|
vegan |
vegan_diversity, vegan_fisher_alpha, vegan_rarefaction |
tabular, png, txt |
an R package fo community ecologist |
2015-08-27 |
https://cran.r-project.org/package=vegan |
2.4-3 |
r-vegan |
2.3_4 |
To update |
Metagenomics |
Standardisation and normalisation, Analysis |
Standardisation and normalisation, Analysis |
Ecology, Phylogenetics, Environmental science |
Ecology, Phylogenetics, Environmental science |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan |
vegan |
vegan |
Ordination methods, diversity analysis and other functions for community and vegetation ecologists |
|
3 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
0 |
101 |
116 |
2314 |
2547 |
167 |
318 |
3493 |
5788 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8335 |
5807 |
434 |
268 |
|
|
True |
False |
|
velvet |
velvetg, velveth |
txt, afg, fasta, tabular, velvet |
de novo genomic assembler specially designed for short read sequencing technologies |
2020-06-09 |
https://www.ebi.ac.uk/~zerbino/velvet/ |
|
velvet |
1.2.10 |
To update |
Assembly |
Formatting, De-novo assembly |
Formatting, De-novo assembly |
Sequence assembly |
Sequence assembly |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet |
velvet |
Velvet |
A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. |
|
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
0 |
2567 |
2888 |
27621 |
32158 |
4951 |
5263 |
52855 |
57273 |
2097 |
2221 |
30746 |
33121 |
109 |
109 |
1097 |
1097 |
123649 |
112319 |
10481 |
9724 |
https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=56edd22d14392691, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=b7c2440621968526, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.org.au/published/workflow?id=30430b75d05f54eb, https://usegalaxy.org.au/published/workflow?id=533dbb3242ee4255, https://usegalaxy.org.au/published/workflow?id=7fa13ccbf044edc5, https://usegalaxy.org.au/published/workflow?id=83e3ceceb1a92493, https://usegalaxy.org.au/published/workflow?id=874492eb776ba813, https://usegalaxy.org.au/published/workflow?id=8b6739a000780d99, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=9b75924c483b5f6b, https://usegalaxy.org.au/published/workflow?id=aee5b5645c51cac3, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org.au/published/workflow?id=ee7a1615f187391d, https://usegalaxy.org.au/published/workflow?id=f25a05070bf97ded, https://usegalaxy.org.au/published/workflow?id=fb0986a952c35e0a, https://usegalaxy.org/published/workflow?id=109092d8dbda4398, https://usegalaxy.org/published/workflow?id=1c7af480caf150bd, https://usegalaxy.org/published/workflow?id=3cf46c167ccb374f, https://usegalaxy.org/published/workflow?id=4e1ae78405034ad3, https://usegalaxy.org/published/workflow?id=51c485af11d90700, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=c30f6ca171896908, https://usegalaxy.org/published/workflow?id=e2ab3d3219a648a7, https://usegalaxy.org/published/workflow?id=e745c45651d829b8, https://usegalaxy.org/published/workflow?id=f6bd33dedc7c6c12, https://usegalaxy.org/published/workflow?id=f926e70bee242785, https://workflowhub.eu/workflows/1622?version=1, https://workflowhub.eu/workflows/2048?version=1 |
assembly/debruijn-graph-assembly, assembly/general-introduction |
True |
False |
|
vibrant |
vibrant |
txt, fasta, genbank, tabular |
Virus Identification By iteRative ANnoTation |
2024-09-11 |
https://github.com/AnantharamanLab/VIBRANT |
1.2.1 |
vibrant |
1.2.1 |
Up-to-date |
Metagenomics |
Sequence trimming, Scaffolding, Genome annotation |
Sequence trimming, Scaffolding, Genome annotation |
Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism |
Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant |
VIBRANT |
VIBRANT |
Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions |
|
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
65 |
65 |
1586 |
1586 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1586 |
1586 |
65 |
65 |
https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 |
|
True |
False |
|
viralverify |
viralverify |
fasta, csv, txt, genbank |
Contigs prediction as viral, chromosomal, plasmidic or uncertain. |
2025-07-04 |
https://github.com/ablab/viralVerify |
1.1 |
viralverify |
1.1 |
Up-to-date |
Sequence Analysis, Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
virannot |
virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv |
tabular, xlsx, zip |
virAnnot wrappers |
2025-08-04 |
https://github.com/marieBvr/virAnnot |
1.2.0 |
biopython |
1.70 |
To update |
Metagenomics |
Sequence annotation, Sequence clustering, Sequence cluster visualisation |
Sequence annotation, Sequence clustering, Sequence cluster visualisation |
Metagenomics, Virology, Microbial ecology |
Metagenomics, Virology, Microbial ecology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot |
virannot |
virAnnot |
VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project "Plant Health Bioinformatics Network". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy. |
|
0 |
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
336 |
336 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
14 |
14 |
350 |
350 |
18 |
18 |
https://usegalaxy.eu/published/workflow?id=17f73aba442315e6, https://usegalaxy.eu/published/workflow?id=86465932556bc96c |
|
True |
False |
|
virsorter |
virsorter |
fasta, tabular, txt |
VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. |
2024-06-20 |
https://github.com/jiarong/VirSorter2/ |
2.2.4 |
virsorter |
2.2.4 |
Up-to-date |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Metagenomics |
Metagenomics |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter |
virsorter |
virsorter |
Identify DNA and RNA virus sequences. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
144 |
144 |
2379 |
2379 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2379 |
2379 |
144 |
144 |
https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95 |
|
True |
False |
|
vrhyme |
vrhyme |
tabular, txt, fasta |
Tool for dereplication and binning virus genomes from metagenomes. |
2025-05-14 |
https://github.com/AnantharamanLab/vRhyme |
1.1.0 |
vrhyme |
1.1.0 |
Up-to-date |
Metagenomics |
Scaffolding, Read binning, Read mapping, Sequence trimming |
Scaffolding, Read binning, Read mapping, Sequence trimming |
Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly |
Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme |
https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme |
vRhyme |
vRhyme |
vRhyme enables binning of viral genomes from metagenomes. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
47 |
47 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
47 |
47 |
6 |
6 |
https://usegalaxy.eu/published/workflow?id=62392daea25a3980 |
|
True |
False |
|
vsearch |
vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting |
fasta, tabular |
VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. |
2014-11-30 |
https://github.com/torognes/vsearch |
2.8.3 |
vsearch |
2.30.4 |
To update |
Sequence Analysis |
DNA mapping, Chimera detection |
DNA mapping, Chimera detection |
Metagenomics, Sequence analysis |
Metagenomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch |
vsearch |
VSEARCH |
High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. |
|
8 |
8 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
0 |
0 |
8 |
8 |
8 |
0 |
226 |
259 |
13600 |
15795 |
323 |
642 |
14828 |
59476 |
82 |
97 |
6641 |
7811 |
11 |
12 |
285 |
286 |
83368 |
35354 |
1010 |
642 |
https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1 |
|
True |
False |