|
CRSConverter |
crsconverter |
xml, shp |
Tools to transforms geographical vector data to a specified coordinate reference system. |
2025-05-20 |
https://github.com/Morphy427/phylodiversity_workflow/CRSConverter |
1.1 |
r-sf |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/CRSConverter |
|
|
|
|
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 |
3 |
3 |
47 |
47 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
47 |
47 |
3 |
3 |
https://usegalaxy.eu/published/workflow?id=89525918b2a32023 |
ecology/phylodiversity_workflow |
True |
False |
|
EstimEndem |
estimate_endem |
shp |
Tools to estimates the endemism of each cell in a spatial grid. |
2025-05-20 |
https://github.com/Morphy427/phylodiversity_workflow/EstimEndem |
0.1.1+galaxy0 |
r-phyloregion |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/EstimEndem |
|
|
|
|
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 |
3 |
3 |
40 |
40 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
40 |
40 |
3 |
3 |
https://usegalaxy.eu/published/workflow?id=89525918b2a32023 |
ecology/phylodiversity_workflow |
True |
False |
|
Geometric means (Dead wood) |
Map_shp, Mean_geom, bar_plot |
pdf, csv, tabular |
Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). |
2023-11-10 |
https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom |
0.1.0+galaxy0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow |
|
|
|
|
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 |
0 |
0 |
0 |
60 |
60 |
163 |
163 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
20 |
20 |
183 |
183 |
62 |
62 |
|
|
True |
False |
|
PylOccuMatcher |
phylogenetic_occupancy_matcher |
newick, tabular |
Tools to matches phylogenetic data with occupancy data. |
2025-05-20 |
https://github.com/Morphy427/phylodiversity_workflow/PhylOccuMatcher |
1.0 |
r-phyloregion |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/PhylOccuMatcher |
|
|
|
|
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 |
4 |
4 |
22 |
22 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
22 |
4 |
4 |
https://usegalaxy.eu/published/workflow?id=89525918b2a32023 |
ecology/phylodiversity_workflow |
True |
False |
|
PyloIndex |
phylo_index |
tabular |
Tools to computes the phylodiversity index. |
2025-05-20 |
https://github.com/Morphy427/phylodiversity_workflow/PyloIndex |
1.0 |
r-phyloregion |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/PhyloIndex |
|
|
|
|
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 |
5 |
5 |
18 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
5 |
5 |
https://usegalaxy.eu/published/workflow?id=89525918b2a32023 |
ecology/phylodiversity_workflow |
True |
False |
|
WormsMeasurements |
WormsMeasurements |
tabular |
This tool uses WoRMS (World Register of Marine Species) to add measurement values to a dataset based on scientific names. |
2025-05-07 |
https://github.com/jeanlecras/tools-ecology |
0.1.2 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/WormsMeasurements |
|
|
|
|
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 |
4 |
4 |
97 |
97 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
97 |
97 |
4 |
4 |
https://usegalaxy.eu/published/workflow?id=749bb05ec8674bec |
ecology/ecoregiolifetraits |
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 |
1 |
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 |
2 |
2 |
3 |
3 |
3 |
3 |
2 |
2 |
|
|
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 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
1258 |
1368 |
7148 |
7779 |
183 |
414 |
505 |
1305 |
398 |
398 |
2608 |
2608 |
11 |
11 |
16 |
16 |
11708 |
10277 |
2191 |
1850 |
|
|
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 |
0 |
0 |
0 |
|
|
True |
True |
|
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 |
0 |
0 |
0 |
165 |
176 |
6369 |
6769 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6769 |
6369 |
176 |
165 |
|
|
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 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1714 |
1714 |
108307 |
108307 |
804 |
804 |
27569 |
27569 |
265 |
265 |
8873 |
8873 |
59 |
59 |
12432 |
12432 |
157181 |
157181 |
2842 |
2842 |
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=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=47e14222073e7192, 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=884a4415b669690c, https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=bb63b5bb983fd49c, https://usegalaxy.eu/published/workflow?id=c14d2e8b3c191bc4, https://usegalaxy.eu/published/workflow?id=c930a54a30dcc7e3, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=ebb131f2a6172081, https://usegalaxy.fr/published/workflow?id=3d3b40398d1cd1ae, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, 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=9ba6da7dae465d3e, https://usegalaxy.org/published/workflow?id=9f68718f025bed30, https://usegalaxy.org/published/workflow?id=b6a795834009ce06, https://usegalaxy.org/published/workflow?id=bdd7011a908bc1aa, 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/1199?version=2, https://workflowhub.eu/workflows/1470?version=2, 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, microbiome/taxonomic-profiling, sequence-analysis/quality-contamination-control |
True |
False |
|
braker3 |
braker3 |
gtf, gff3 |
BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . |
2023-06-13 |
https://github.com/Gaius-Augustus/BRAKER |
3.0.8 |
|
|
To update |
Genome annotation |
Genome annotation, Gene prediction |
Genome annotation, Gene prediction |
RNA-Seq, Genomics, Structure prediction, Sequence analysis |
RNA-Seq, Genomics, Structure prediction, Sequence analysis |
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/braker |
https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 |
braker3 |
BRAKER3 |
BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes |
|
1 |
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 |
1 |
1 |
0 |
711 |
711 |
5354 |
5354 |
0 |
0 |
0 |
0 |
135 |
135 |
987 |
987 |
26 |
26 |
275 |
275 |
6616 |
6616 |
872 |
872 |
https://workflowhub.eu/workflows/1509?version=1, https://workflowhub.eu/workflows/1746?version=1, https://workflowhub.eu/workflows/2029?version=1 |
genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation |
True |
False |
|
champ_blocs |
cb_dissim, cb_ivr, cb_div |
rdata, tabular |
Compute indicators for turnover boulders fields |
2022-10-28 |
|
0.0.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/Marie59/champ_blocs |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs |
|
|
|
|
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 |
0 |
3 |
0 |
9 |
9 |
216 |
216 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
11 |
11 |
227 |
227 |
11 |
11 |
https://usegalaxy.eu/published/workflow?id=a3ad27817f77061b, https://workflowhub.eu/workflows/1690?version=1, https://workflowhub.eu/workflows/661?version=1 |
ecology/champs-blocs |
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 |
1.38.0 |
bioconductor-dada2 |
1.38.0 |
Up-to-date |
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 |
0 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
10 |
865 |
885 |
205808 |
209081 |
1301 |
1344 |
254475 |
270135 |
179 |
179 |
52639 |
52639 |
72 |
72 |
38131 |
38131 |
569986 |
551053 |
2480 |
2417 |
https://usegalaxy.eu/published/workflow?id=48d0dc424e71d8c2, https://usegalaxy.eu/published/workflow?id=642f4c47028031d7, https://usegalaxy.eu/published/workflow?id=7b557efda89bb998, https://usegalaxy.eu/published/workflow?id=b483cf6a138d2372, https://usegalaxy.eu/published/workflow?id=e132370adf8f2838, https://usegalaxy.eu/published/workflow?id=e3918808605cf8cd, https://usegalaxy.fr/published/workflow?id=b5d86d505c09d170, https://usegalaxy.org.au/published/workflow?id=1016f17b77a8216d, https://usegalaxy.org.au/published/workflow?id=2d05f15a9616cc47, https://usegalaxy.org.au/published/workflow?id=400fbd96fb04c60e, https://usegalaxy.org/published/workflow?id=0942f2f3386e6b41, https://usegalaxy.org/published/workflow?id=38f9fc867c4d1f40, https://usegalaxy.org/published/workflow?id=4faff660f6defa10, https://usegalaxy.org/published/workflow?id=5df593510c7d944d, https://usegalaxy.org/published/workflow?id=78e60413358273bc, https://usegalaxy.org/published/workflow?id=806ef8816168916f, https://usegalaxy.org/published/workflow?id=e067c4e66f0af362, https://usegalaxy.org/published/workflow?id=ecf3a7f9da7409ef, https://workflowhub.eu/workflows/1395?version=2, https://workflowhub.eu/workflows/790?version=3 |
microbiome/dada-16S |
True |
True |
|
data_exploration |
tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs |
tabular, txt, Rdata, png |
Explore data through multiple statistical tools |
2021-06-23 |
|
0.0.0 |
r-tangles |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/Marie59/Data_explo_tools |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration |
|
|
|
|
0 |
0 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
0 |
122 |
122 |
1286 |
1286 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
44 |
44 |
1330 |
1330 |
128 |
128 |
https://usegalaxy.eu/published/workflow?id=7b576a562031ff7e, https://usegalaxy.eu/published/workflow?id=a0404f6291874c01, https://workflowhub.eu/workflows/1693?version=1, https://workflowhub.eu/workflows/656?version=1 |
ecology/biodiversity-data-exploration |
True |
False |
|
earth |
landcover_subindicator |
shp |
Access, process, visualise oceanographic data for the Earth System |
2024-10-21 |
https://github.com/Marie59/FE-ft-ESG/tree/main/earth |
0.1.0 |
numpy |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth |
|
|
|
|
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 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1 |
|
|
True |
False |
|
ecoregionalization |
ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ClaraGuess, ecoregion_clara_cluster, ecoregion_eco_map, indicspecies, ecoregion_taxa_seeker |
tabular, png, txt |
Tools to compute ecoregionalization with BRT model predictions and clustering. |
2023-07-26 |
https://github.com/PaulineSGN/Workflow_Galaxy |
0.1.2+galaxy0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow |
|
|
|
|
0 |
0 |
8 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
5 |
0 |
13 |
13 |
987 |
987 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
987 |
987 |
13 |
13 |
https://usegalaxy.eu/published/workflow?id=749bb05ec8674bec, https://usegalaxy.eu/published/workflow?id=89ff2a1143954d83, https://usegalaxy.eu/published/workflow?id=b727b64f37238fff, https://usegalaxy.eu/published/workflow?id=c5de0b794849e1b1, https://workflowhub.eu/workflows/1208?version=1, https://workflowhub.eu/workflows/1209?version=1, https://workflowhub.eu/workflows/1680?version=1, https://workflowhub.eu/workflows/658?version=1 |
ecology/Ecoregionalization_tutorial, ecology/ecoregiolifetraits |
True |
False |
|
emlassemblyline |
annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template |
txt, xml |
Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa |
2023-07-21 |
https://github.com/EDIorg/EMLassemblyline |
0.1.2+galaxy0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline |
|
|
|
|
0 |
0 |
11 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
40 |
40 |
646 |
646 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
648 |
648 |
41 |
41 |
https://usegalaxy.eu/published/workflow?id=a30d511e3dda0895, https://usegalaxy.eu/published/workflow?id=ab89c61db3d7abbb |
|
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 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
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 |
|
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 |
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 |
|
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 |
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 |
|
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 |
0 |
0 |
0 |
0 |
5 |
5 |
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 |
|
gdal |
gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo |
tiff, xml, txt, json, tabular, csv, shp |
Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. |
2019-02-25 |
https://www.gdal.org |
3.0.0 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal |
|
|
|
|
0 |
0 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
8 |
8 |
11 |
15 |
724 |
1525 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
3 |
3 |
1528 |
727 |
17 |
13 |
https://usegalaxy.eu/published/workflow?id=3b0803542deff026, https://usegalaxy.eu/published/workflow?id=b0b6c8756070650b, https://workflowhub.eu/workflows/1670?version=1, https://workflowhub.eu/workflows/404?version=1 |
ecology/gbif_cleaning |
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 |
0 |
1 |
0 |
0 |
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 |
|
getorganelle |
get_annotated_regions_from_gb, get_organelle_from_reads |
fasta, txt, gfa1, fastg, tsv, fastq, sam |
GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. |
2022-03-15 |
https://github.com/Kinggerm/GetOrganelle |
1.7.7.1 |
getorganelle |
1.7.7.1 |
Up-to-date |
Assembly |
De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming |
De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming |
Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms |
Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle |
getorganelle |
GetOrganelle |
A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. |
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
403 |
403 |
9423 |
9423 |
0 |
0 |
0 |
0 |
108 |
108 |
1588 |
1588 |
0 |
0 |
0 |
0 |
11011 |
11011 |
511 |
511 |
https://usegalaxy.org.au/published/workflow?id=f2541030f6d70b59 |
|
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 |
0 |
2 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
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 |
|
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 |
0 |
1 |
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 |
|
hapcut2 |
hapcut2 |
txt, vcf |
Robust and accurate haplotype assembly for diverse sequencing technologies |
2022-10-19 |
https://github.com/vibansal/HapCUT2 |
1.3.4 |
hapcut2 |
1.3.4 |
Up-to-date |
Assembly |
Haplotype mapping, Variant classification |
Haplotype mapping, Variant classification |
|
|
galaxy-australia |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 |
hapcut2 |
HapCUT2 |
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md |
|
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 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
131 |
131 |
0 |
0 |
0 |
0 |
131 |
131 |
6 |
6 |
|
|
True |
False |
|
hapog |
hapog |
fasta, tsv |
Hapo-G - Haplotype-Aware Polishing of Genomes |
2022-09-16 |
https://github.com/institut-de-genomique/HAPO-G |
1.3.8 |
hapog |
1.3.8 |
Up-to-date |
Assembly |
Genome assembly, Optimisation and refinement |
Genome assembly, Optimisation and refinement |
Sequence assembly, Genomics |
Sequence assembly, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog |
hapog |
Hapo-G |
Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. |
|
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 |
0 |
1 |
0 |
94 |
94 |
677 |
677 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
36 |
36 |
392 |
392 |
1069 |
1069 |
130 |
130 |
|
|
True |
False |
|
helixer |
helixer |
gff3 |
Gene calling with Deep Neural Networks |
2023-06-14 |
https://github.com/weberlab-hhu/Helixer |
0.3.6 |
|
|
To update |
Genome annotation |
Gene prediction, Genome annotation |
Gene prediction, Genome annotation |
Sequence analysis, Gene transcripts |
Sequence analysis, Gene transcripts |
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/helixer |
https://github.com/genouest/galaxy-tools/tree/master/tools/helixer |
helixer |
Helixer |
Deep Learning to predict gene annotations |
|
1 |
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 |
1 |
1 |
0 |
161 |
161 |
1024 |
1024 |
56 |
56 |
184 |
184 |
51 |
51 |
385 |
385 |
25 |
25 |
363 |
363 |
1956 |
1956 |
293 |
293 |
https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=6550f72070b24082, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d, https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b, https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177, https://usegalaxy.org/published/workflow?id=4605309321799e9b, https://usegalaxy.org/published/workflow?id=80a7124c40438cc9, https://usegalaxy.org/published/workflow?id=f4111a169255535c, https://workflowhub.eu/workflows/1255?version=3, https://workflowhub.eu/workflows/1500?version=1, https://workflowhub.eu/workflows/1746?version=1 |
genome-annotation/comparison-braker-helixer-annotation, genome-annotation/helixer |
True |
False |
|
hifiasm |
hifiasm |
gfa1, txt |
A fast haplotype-resolved de novo assembler |
2024-07-11 |
https://github.com/chhylp123/hifiasm |
0.25.0 |
hifiasm |
0.25.0 |
Up-to-date |
Assembly |
|
|
|
|
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm |
|
|
|
|
1 |
1 |
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 |
1 |
1 |
803 |
803 |
2713 |
2713 |
585 |
585 |
2136 |
2136 |
187 |
187 |
3817 |
3817 |
51 |
51 |
183 |
183 |
8849 |
8849 |
1626 |
1626 |
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assembly/hifi-assembly, assembly/vgp_genome_assembly |
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 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
40 |
40 |
229 |
229 |
0 |
0 |
0 |
0 |
16 |
16 |
368 |
368 |
0 |
0 |
0 |
0 |
597 |
597 |
56 |
56 |
|
|
True |
False |
|
hirondelle_crim_ogc_api_processes |
hirondelle_crim |
txt |
This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. |
2024-06-07 |
https://github.com/AquaINFRA/galaxy |
0.2.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes |
|
|
|
|
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 |
4 |
4 |
237 |
237 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
237 |
237 |
4 |
4 |
https://usegalaxy.eu/published/workflow?id=6173008772bdba09, https://usegalaxy.eu/published/workflow?id=b1fa4a3561988704 |
|
True |
False |
|
hisat2 |
hisat2 |
bam, fastqsanger, txt, tabular |
HISAT2 is a fast and sensitive spliced alignment program. |
2015-09-29 |
http://ccb.jhu.edu/software/hisat2/ |
2.2.2 |
hisat2 |
2.2.2 |
Up-to-date |
Assembly |
Sequence alignment |
Sequence alignment |
RNA-seq |
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 |
hisat2 |
HISAT2 |
Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). |
|
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 |
1 |
1 |
1 |
12585 |
14119 |
420921 |
467443 |
28716 |
40390 |
729970 |
1057729 |
5266 |
6509 |
88398 |
111027 |
1273 |
1277 |
52049 |
52136 |
1688335 |
1291338 |
62295 |
47840 |
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proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation, transcriptomics/de-novo, transcriptomics/minerva-pathways, transcriptomics/rna-seq-reads-to-counts, transcriptomics/srna |
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 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
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 |
|
interpolation |
interpolation_run_idw_interpolation |
png |
Run IDW interpolation based on a .csv and .geojson file |
2024-01-05 |
https://github.com/AquaINFRA/galaxy |
1.0 |
r-getopt |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation |
|
|
|
|
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 |
7 |
7 |
70 |
70 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
70 |
70 |
7 |
7 |
https://usegalaxy.eu/published/workflow?id=0b2304aa2083bd1a, https://workflowhub.eu/workflows/807?version=1 |
|
True |
False |
|
iphop |
iphop_predict |
csv |
Integrated Phage Host Prediction |
2024-10-14 |
https://bitbucket.org/srouxjgi/iphop/ |
1.4.2 |
iphop |
1.4.2 |
Up-to-date |
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 |
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 |
|
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. |
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1 |
1 |
1 |
0 |
0 |
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0 |
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0 |
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1 |
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0 |
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1 |
1 |
369 |
369 |
4901 |
4901 |
0 |
0 |
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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. |
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5 |
0 |
0 |
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2 |
2 |
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0 |
0 |
2 |
2 |
2 |
2 |
|
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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 |
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 |
|
lca_wrapper |
lca1 |
taxonomy |
Find lowest diagnostic rank |
2014-01-27 |
https://bitbucket.org/natefoo/taxonomy |
1.0.1 |
taxonomy |
0.10.4 |
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 |
|
|
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1 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3 |
20 |
11 |
137 |
14 |
1112 |
112 |
6136 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6273 |
123 |
1132 |
17 |
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|
True |
False |
|
links |
links |
fasta, tabular, graph_dot |
Scaffold genome assemblies with long reads. |
2022-02-23 |
https://github.com/bcgsc/LINKS |
2.0.1 |
links |
2.0.1 |
Up-to-date |
Assembly |
Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming |
Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming |
Sequence assembly, Mapping, Sequencing |
Sequence assembly, Mapping, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/links |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/links |
links |
LINKS |
LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
181 |
181 |
940 |
940 |
0 |
0 |
0 |
0 |
87 |
87 |
778 |
778 |
0 |
0 |
0 |
0 |
1718 |
1718 |
268 |
268 |
|
|
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 |
1 |
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 |
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 |
|
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 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
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 |
0 |
0 |
0 |
0 |
1 |
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 |
4 |
4 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
4 |
2 |
49 |
57 |
10768 |
10867 |
18 |
18 |
922 |
922 |
18 |
18 |
3187 |
3187 |
3 |
3 |
29 |
29 |
15005 |
14906 |
96 |
88 |
|
|
True |
False |
|
mean_per_zone |
mean_per_zone |
png |
Creates a png image showing statistic over areas as defined in the vector file |
2019-03-15 |
https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ |
0.2.0 |
python |
|
To update |
Visualization, GIS, Climate Analysis |
|
|
|
|
climate |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone |
|
|
|
|
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 |
1 |
1 |
1 |
3 |
1 |
25 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
25 |
1 |
3 |
1 |
|
|
True |
False |
|
medenv |
iabiodiv_smartbiodiv_med_environ |
tabular |
Retrieve environmental data from etopo, cmems and woa |
2023-11-30 |
https://github.com/jeremyfix/medenv |
0.1.2 |
pandas |
|
To update |
Ecology, Data Source |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv |
|
|
|
|
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 |
11 |
11 |
38 |
38 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
38 |
38 |
11 |
11 |
|
|
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 |
0 |
0 |
0 |
0 |
2 |
2 |
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 |
|
merquryfk |
merquryfk_asmplot, merquryfk_cnplot, merquryfk_hapmaker, merquryfk_happlot, merquryfk_merquryfk |
fastk_ktab, fastk_ktab_tar, png, pdf, tabular, bed |
FastK based version of Merqury |
2025-02-11 |
https://github.com/thegenemyers/MERQURY.FK |
1.1.1 |
merquryfk |
1.2 |
To update |
Sequence Analysis, Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/merquryfk |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/merquryfk |
|
|
|
|
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 |
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 |
|
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 |
1.1.1 |
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 |
0 |
0 |
0 |
|
|
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 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
15 |
23 |
521 |
763 |
28 |
56 |
261 |
530 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1293 |
782 |
79 |
43 |
|
|
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 |
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 |
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 |
|
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 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
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 |
|
mitobim |
mitobim |
fasta |
assemble mitochondrial genomes |
2020-12-29 |
https://github.com/chrishah/MITObim |
1.9.1 |
mitobim |
1.9.1 |
Up-to-date |
Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
168 |
168 |
1463 |
1463 |
0 |
0 |
0 |
0 |
39 |
39 |
533 |
533 |
0 |
0 |
0 |
0 |
1996 |
1996 |
207 |
207 |
|
|
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 |
0 |
0 |
0 |
0 |
2 |
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=3 |
|
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 |
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 |
|
necat |
necat |
fasta.gz, fasta |
Error correction and de-novo assembly for ONT Nanopore reads |
2021-11-29 |
https://github.com/xiaochuanle/NECAT |
0.0.1_update20200803 |
necat |
0.0.1_update20200803 |
Up-to-date |
Assembly |
De-novo assembly |
De-novo assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat |
necat |
NECAT |
NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. |
|
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 |
0 |
1 |
0 |
228 |
228 |
1106 |
1106 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1106 |
1106 |
228 |
228 |
|
|
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 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1756 |
1893 |
51682 |
53373 |
2196 |
2332 |
18983 |
20195 |
1114 |
1145 |
9635 |
9912 |
48 |
49 |
310 |
312 |
83792 |
80610 |
5419 |
5114 |
https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=b1a799497c366eef, https://usegalaxy.eu/published/workflow?id=c1e26abe61c69688, https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=dadca1020f586338, https://usegalaxy.eu/published/workflow?id=dc57118a95b10a80, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=2717e90438c7fb8c, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3, https://usegalaxy.org.au/published/workflow?id=a52609119b30e64d, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=005924662f68a480, https://usegalaxy.org/published/workflow?id=0596162a499b4074, https://usegalaxy.org/published/workflow?id=0c115bf8a319011c, https://usegalaxy.org/published/workflow?id=16bb8f465e731e0e, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=31b5dd92790dce88, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=6f090b2c259847d2, https://usegalaxy.org/published/workflow?id=775335812a6b7a61, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb, https://usegalaxy.org/published/workflow?id=82cfe6aefc1bf82a, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=ac92a988e550cd23, https://usegalaxy.org/published/workflow?id=bc01b8b203ecc754, https://usegalaxy.org/published/workflow?id=d653eaefcf6b4697, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1418?version=1, https://workflowhub.eu/workflows/1465?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/653?version=1 |
evolution/abc_intro_phylo, microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short, microbiome/pathogen-detection-from-nanopore-foodborne-data |
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 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
16 |
19 |
105 |
195 |
23 |
26 |
122 |
168 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
363 |
227 |
45 |
39 |
|
|
True |
False |
|
obisindicators |
obisindicators, obis_data |
csv, tabular |
Compute biodiveristy indicators for marine data from obis |
2022-11-04 |
https://github.com/Marie59/obisindicators |
0.0.2 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators |
|
|
|
|
1 |
0 |
2 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
1 |
0 |
29 |
29 |
399 |
399 |
15 |
15 |
25 |
25 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
424 |
424 |
44 |
44 |
https://usegalaxy.eu/published/workflow?id=4f51080ffe7d57e0, https://usegalaxy.eu/published/workflow?id=9e05bd65faf58ab3, https://workflowhub.eu/workflows/1698?version=1, https://workflowhub.eu/workflows/662?version=1, https://workflowhub.eu/workflows/758?version=1 |
climate/earth_system, ecology/obisindicators |
True |
False |
|
ocean |
argo_getdata, copernicusmarine, divand_full_analysis |
netcdf |
Access, process, and visualise oceanographic data for the Earth System |
2023-11-17 |
https://github.com/Marie59/FE-ft-ESG/tree/main/ocean |
0.1.15 |
copernicusmarine |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean |
|
|
|
|
0 |
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 |
2 |
0 |
0 |
14 |
14 |
189 |
189 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
189 |
189 |
14 |
14 |
https://usegalaxy.eu/published/workflow?id=26fe6b0fb6ca2892, https://usegalaxy.eu/published/workflow?id=a80f9b926ba43892, https://usegalaxy.eu/published/workflow?id=fc33ea1679e5f1b7, https://workflowhub.eu/workflows/1436?version=1, https://workflowhub.eu/workflows/1445?version=1 |
climate/argo_pangeo, climate/earth_system, climate/ocean-variables |
True |
False |
|
ogcProcess_otb_bandmath |
otb_band_math |
png |
Outputs a monoband image which is the result of a mathematical operation on several multi-band images. |
2024-03-12 |
https://github.com/AquaINFRA/galaxy |
1.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath |
|
|
|
|
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 |
8 |
8 |
100 |
100 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
100 |
100 |
8 |
8 |
https://usegalaxy.eu/published/workflow?id=b1fa4a3561988704, https://usegalaxy.eu/published/workflow?id=e8244d1c80ea0470 |
|
True |
False |
|
ogcProcess_otb_meanShiftSmoothing |
otb_mean_shift_smoothing |
|
This application smooths an image using the MeanShift algorithm. |
2024-03-12 |
https://github.com/AquaINFRA/galaxy |
1.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing |
|
|
|
|
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 |
4 |
4 |
57 |
57 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
57 |
57 |
4 |
4 |
https://usegalaxy.eu/published/workflow?id=e8244d1c80ea0470 |
|
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 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
4 |
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 |
|
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 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
1 |
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 |
|
|
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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 |
0 |
0 |
0 |
https://usegalaxy.eu/published/workflow?id=c62d65832377e376 |
|
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 |
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 |
|
|
True |
False |
|
prinseq |
prinseq |
|
PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets |
2016-05-30 |
http://prinseq.sourceforge.net/manual.html |
@TOOL_VERSION+galaxy2 |
prinseq |
0.20.4 |
To update |
Fastq Manipulation, Metagenomics |
Read pre-processing, Sequence trimming, Sequence contamination filtering |
Read pre-processing, Sequence trimming, Sequence contamination filtering |
Transcriptomics, Metagenomics, Genomics |
Transcriptomics, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq |
prinseq |
PRINSEQ |
PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. |
|
1 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
345 |
412 |
15643 |
16651 |
1317 |
1501 |
10523 |
12474 |
0 |
0 |
0 |
0 |
11 |
11 |
17 |
17 |
29142 |
26183 |
1924 |
1673 |
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microbiome/mgnify-amplicon |
True |
False |
|
purge_dups |
purge_dups |
tabular, wig, png, txt, bed |
Purge haplotigs and overlaps in an assembly based on read depth |
2021-02-03 |
https://github.com/dfguan/purge_dups |
1.2.6 |
purge_dups |
1.2.6 |
Up-to-date |
Assembly |
Genome assembly, Read binning, Scaffolding |
Genome assembly, Read binning, Scaffolding |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups |
purge_dups |
purge_dups |
Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences |
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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 |
1 |
1 |
0 |
365 |
365 |
19303 |
19303 |
97 |
97 |
1776 |
1776 |
80 |
80 |
3001 |
3001 |
0 |
0 |
0 |
0 |
24080 |
24080 |
542 |
542 |
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assembly/vgp_genome_assembly |
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 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
11028 |
11672 |
120605 |
126603 |
13078 |
14773 |
78457 |
86986 |
4849 |
5353 |
46644 |
50987 |
613 |
619 |
14902 |
14963 |
279539 |
260608 |
32417 |
29568 |
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https://usegalaxy.org/published/workflow?id=e2ab3d3219a648a7, https://usegalaxy.org/published/workflow?id=e745c45651d829b8, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://usegalaxy.org/published/workflow?id=f926e70bee242785, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1580?version=1, https://workflowhub.eu/workflows/1595?version=1, https://workflowhub.eu/workflows/1598?version=1, https://workflowhub.eu/workflows/1602?version=2, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/1613?version=2, https://workflowhub.eu/workflows/1621?version=1, https://workflowhub.eu/workflows/1622?version=1, https://workflowhub.eu/workflows/1634?version=1, https://workflowhub.eu/workflows/1646?version=1, https://workflowhub.eu/workflows/1882?version=3, https://workflowhub.eu/workflows/2011?version=1, https://workflowhub.eu/workflows/2024?version=3, 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=4, 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 |
1 |
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 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
True |
False |
|
ragtag |
ragtag |
paf, agp, fasta, txt, tabular |
Reference-guided scaffolding of draft genomes tool. |
2021-11-10 |
https://github.com/malonge/RagTag |
2.1.0 |
ragtag |
2.1.0 |
Up-to-date |
Assembly |
Genome assembly |
Genome assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag |
ragtag |
ragtag |
RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. |
|
1 |
1 |
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 |
1 |
1 |
774 |
774 |
8106 |
8106 |
6 |
6 |
59 |
59 |
108 |
108 |
2145 |
2145 |
32 |
32 |
416 |
416 |
10726 |
10726 |
920 |
920 |
https://usegalaxy.org.au/published/workflow?id=7f37c5366bce5489 |
|
True |
False |
|
raven |
raven |
gfa1, fasta |
Raven is a de novo genome assembler for long uncorrected reads. |
2020-11-04 |
https://github.com/lbcb-sci/raven |
1.8.3 |
raven-assembler |
1.8.3 |
Up-to-date |
Assembly |
De-novo assembly, Genome assembly, Read pre-processing |
De-novo assembly, Genome assembly, Read pre-processing |
Sequence assembly, Whole genome sequencing, Genomics |
Sequence assembly, Whole genome sequencing, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven |
raven |
Raven |
a de novo genome assembler for long reads.Raven is a de novo genome assembler for long uncorrected reads. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
610 |
610 |
15837 |
15837 |
0 |
0 |
0 |
0 |
276 |
276 |
13041 |
13041 |
24 |
24 |
217 |
217 |
29095 |
29095 |
910 |
910 |
|
|
True |
False |
|
regionalgam |
regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend |
tabular, png, txt, rdata |
|
2019-06-18 |
https://github.com/RetoSchmucki/regionalGAM |
1.5 |
r-mgcv |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam |
|
|
|
|
0 |
0 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
7 |
7 |
18 |
39 |
129 |
547 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
547 |
129 |
39 |
18 |
https://usegalaxy.eu/published/workflow?id=8e92a65d3307d87e, https://workflowhub.eu/workflows/1707?version=1 |
ecology/regionalGAM |
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 |
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 |
|
repeatmodeler |
repeatmodeler |
fasta, stockholm |
RepeatModeler - Model repetitive DNA |
2021-08-26 |
https://www.repeatmasker.org/RepeatModeler/ |
2.0.5 |
|
|
To update |
Genome annotation |
Repeat sequence detection |
Repeat sequence detection |
Sequence composition, complexity and repeats, Sequence composition, complexity and repeats |
Sequence composition, complexity and repeats, Sequence composition, complexity and repeats |
csbl |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler |
repeatmodeler |
RepeatModeler |
De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. |
|
1 |
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 |
1 |
1 |
725 |
725 |
9423 |
9423 |
424 |
424 |
2473 |
2473 |
240 |
240 |
8995 |
8995 |
30 |
30 |
270 |
270 |
21161 |
21161 |
1419 |
1419 |
https://usegalaxy.eu/published/workflow?id=09c534f738426a6d, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=f9279495683a8ac3, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a71349ba0bff403a, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=ffb1117077f68a9f, https://usegalaxy.org/published/workflow?id=effc17e170263ae6, https://workflowhub.eu/workflows/575?version=1, https://workflowhub.eu/workflows/875?version=3 |
genome-annotation/repeatmasker |
True |
False |
|
retrieve_bold |
retrieve_bold |
txt |
Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers |
2024-06-21 |
https://anaconda.org/conda-forge/r-bold |
1.3.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/wpearman1996/MARES_database_pipeline/tree/master |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold |
|
|
|
|
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 |
8 |
8 |
15 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
15 |
8 |
8 |
|
|
True |
False |
|
rnaquast |
rna_quast |
txt, tgz, pdf, tabular |
rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. |
2020-10-05 |
https://github.com/ablab/rnaquast |
2.3.2 |
rnaquast |
2.3.2 |
Up-to-date |
Assembly, RNA |
De-novo assembly, Transcriptome assembly, Sequence assembly validation |
De-novo assembly, Transcriptome assembly, Sequence assembly validation |
Sequence assembly, Transcriptomics, RNA-Seq |
Sequence assembly, Transcriptomics, RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast |
rnaQUAST |
rnaQUAST |
Quality assessment tool for de novo transcriptome assemblies. |
|
1 |
1 |
1 |
1 |
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 |
375 |
375 |
1887 |
1887 |
196 |
196 |
767 |
767 |
31 |
31 |
326 |
326 |
11 |
11 |
103 |
103 |
3083 |
3083 |
613 |
613 |
https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://workflowhub.eu/workflows/1688?version=1 |
transcriptomics/differential-isoform-expression |
True |
False |
|
salsa |
salsa |
fasta, agp |
A tool to scaffold long read assemblies with Hi-C |
2021-01-14 |
https://github.com/marbl/SALSA |
2.3 |
salsa2 |
2.3 |
Up-to-date |
Assembly |
Genome assembly, De-novo assembly, Scaffolding |
Genome assembly, De-novo assembly, Scaffolding |
Sequence assembly, DNA binding sites, Mapping |
Sequence assembly, DNA binding sites, Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 |
SALSA |
SALSA |
> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch |
|
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 |
1 |
1 |
0 |
130 |
130 |
495 |
495 |
103 |
103 |
1074 |
1074 |
24 |
24 |
410 |
410 |
0 |
0 |
0 |
0 |
1979 |
1979 |
257 |
257 |
https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467, https://workflowhub.eu/workflows/1607?version=1 |
assembly/vgp_genome_assembly |
True |
False |
|
sample_seqs |
sample_seqs |
|
Sub-sample sequences files (e.g. to reduce coverage) |
2014-02-18 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs |
0.2.6 |
biopython |
1.70 |
To update |
Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs |
https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs |
|
|
|
|
1 |
1 |
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 |
1 |
1 |
376 |
457 |
3760 |
4585 |
274 |
274 |
2029 |
2029 |
54 |
54 |
2601 |
2601 |
9 |
9 |
113 |
113 |
9328 |
8503 |
794 |
713 |
|
transcriptomics/mirna-target-finder |
True |
False |
|
samtools_depad |
samtools_depad |
bam |
Re-align a SAM/BAM file with a padded reference (using samtools depad) |
2014-04-14 |
http://www.htslib.org/ |
0.0.5 |
samtools |
1.23.1 |
To update |
Assembly, SAM, Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad |
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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 |
|
samtools_depth |
samtools_depth |
tabular |
Coverage depth via samtools |
2014-11-19 |
http://www.htslib.org/ |
0.0.3 |
samtools |
1.23.1 |
To update |
Assembly, Sequence Analysis, SAM |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth |
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth |
|
|
|
|
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1071 |
1130 |
8403 |
9175 |
1771 |
1964 |
11692 |
12814 |
99 |
99 |
761 |
761 |
77 |
77 |
151 |
151 |
22901 |
21007 |
3270 |
3018 |
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microbiome/pathogen-detection-from-nanopore-foodborne-data |
True |
False |
|
sdmpredictors |
sdmpredictors_list_layers |
|
Terrestrial and marine predictors for species distribution modelling. |
2024-03-29 |
https://cran.r-project.org/web/packages/sdmpredictors/index.html |
0.2.15 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors |
|
|
|
|
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 |
4 |
4 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
4 |
4 |
|
|
True |
False |
|
seq_primer_clip |
seq_primer_clip |
|
Trim off 5' or 3' primers |
2013-09-26 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip |
0.0.18 |
galaxy_sequence_utils |
1.2.0 |
To update |
Assembly, Fasta Manipulation, Text Manipulation |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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 |
|
shasta |
shasta |
gfa1, txt, csv, fasta |
Fast de novo assembly of long read sequencing data |
2020-11-11 |
https://github.com/chanzuckerberg/shasta |
0.6.0 |
shasta |
0.14.0 |
To update |
Assembly, Nanopore |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta |
|
|
|
|
0 |
1 |
1 |
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 |
399 |
399 |
1291 |
1291 |
0 |
0 |
0 |
0 |
98 |
98 |
791 |
791 |
0 |
0 |
0 |
0 |
2082 |
2082 |
497 |
497 |
|
|
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 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
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 |
|
smudgeplot |
smudgeplot |
png, tabular, txt |
Inference of ploidy and heterozygosity structure using whole genome sequencing |
2022-06-30 |
https://github.com/KamilSJaron/smudgeplot |
0.2.5 |
smudgeplot |
0.5.3 |
To update |
Assembly |
Sequence trimming, Genotyping, k-mer counting |
Sequence trimming, Genotyping, k-mer counting |
Sequence assembly, Genetic variation, Mathematics |
Sequence assembly, Genetic variation, Mathematics |
galaxy-australia |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot |
smudgeplots |
Smudgeplots |
Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 |
|
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 |
1 |
1 |
1 |
146 |
146 |
805 |
805 |
90 |
90 |
242 |
242 |
78 |
78 |
1315 |
1315 |
0 |
0 |
0 |
0 |
2362 |
2362 |
314 |
314 |
https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1641?version=1, https://workflowhub.eu/workflows/603?version=2, https://workflowhub.eu/workflows/698?version=1 |
assembly/ERGA-post-assembly-QC |
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 |
1 |
0 |
0 |
0 |
0 |
0 |
2 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
3 |
9 |
3 |
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 |
|
spaln |
list_spaln_tables, spaln |
tabular |
Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. |
2019-01-11 |
https://github.com/ogotoh/spaln |
2.4.9 |
python |
|
To update |
Sequence Analysis, Genome annotation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln |
|
|
|
|
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
110 |
132 |
399 |
612 |
267 |
318 |
4249 |
4506 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5118 |
4648 |
450 |
377 |
|
|
True |
False |
|
spocc_occ |
spocc_occ |
tabular |
Get species occurences data |
2019-05-23 |
https://cran.r-project.org/web/packages/spocc/index.html |
1.2.2 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc |
|
|
|
|
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 |
1 |
1 |
1 |
123 |
146 |
706 |
976 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
28 |
28 |
1004 |
734 |
158 |
135 |
https://usegalaxy.eu/published/workflow?id=3b0803542deff026, https://usegalaxy.eu/published/workflow?id=b0b6c8756070650b, https://workflowhub.eu/workflows/1670?version=1, https://workflowhub.eu/workflows/1687?version=1, https://workflowhub.eu/workflows/404?version=1 |
climate/earth_system, ecology/gbif_cleaning, ecology/species-distribution-modeling |
True |
False |
|
srs_tools |
srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata |
tabular, csv, zip, txt |
Compute biodiversity indicators for remote sensing data from Sentinel 2 |
2022-11-16 |
|
0.0.1 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/Marie59/Sentinel_2A/srs_tools |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools |
|
|
|
|
4 |
0 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
7 |
0 |
8 |
8 |
274 |
274 |
5 |
5 |
48 |
48 |
0 |
0 |
0 |
0 |
3 |
3 |
22 |
22 |
344 |
344 |
16 |
16 |
https://usegalaxy.eu/published/workflow?id=1d2cd0af01a30a46, https://usegalaxy.eu/published/workflow?id=da88448ab15d167d, https://workflowhub.eu/workflows/1669?version=2, https://workflowhub.eu/workflows/657?version=1 |
ecology/remote-sensing |
True |
False |
|
stoceps |
stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic |
tabular, png |
Tools to analyse STOC data. |
2019-09-26 |
|
0.0.2 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc |
|
|
|
|
0 |
0 |
5 |
5 |
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 |
24 |
26 |
180 |
354 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
354 |
180 |
26 |
24 |
https://usegalaxy.eu/published/workflow?id=01274dfdbdfcaa88 |
|
True |
False |
|
taxonomy_filter_refseq |
taxonomy_filter_refseq |
fasta |
Filter RefSeq by taxonomy |
2019-01-13 |
https://github.com/pvanheus/ncbitaxonomy |
0.3.0 |
rust-ncbitaxonomy |
1.0.7 |
To update |
Sequence Analysis, Genome annotation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq |
|
|
|
|
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 |
0 |
0 |
0 |
|
|
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 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
1 |
7406 |
7874 |
48617 |
51653 |
6438 |
7659 |
33268 |
41191 |
2005 |
2042 |
11003 |
11192 |
162 |
163 |
565 |
586 |
104622 |
93453 |
17738 |
16011 |
https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=0590554db9794d13, https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=0bafeb17c21ebc9c, https://usegalaxy.eu/published/workflow?id=10101558b211a782, https://usegalaxy.eu/published/workflow?id=14714876dda7186d, https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=379ea60fe05ce9e3, https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, 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https://usegalaxy.org/published/workflow?id=bc01b8b203ecc754, https://usegalaxy.org/published/workflow?id=c3ea8fa3bb202dc6, https://usegalaxy.org/published/workflow?id=cade0c5c11978323, https://usegalaxy.org/published/workflow?id=d5436cee11a34de9, https://usegalaxy.org/published/workflow?id=d653eaefcf6b4697, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/101?version=1, https://workflowhub.eu/workflows/1059?version=1, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/124?version=1, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/1439?version=1, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1465?version=1, https://workflowhub.eu/workflows/1466?version=2, https://workflowhub.eu/workflows/1470?version=2, https://workflowhub.eu/workflows/1472?version=1, https://workflowhub.eu/workflows/1473?version=1, https://workflowhub.eu/workflows/1483?version=1, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1, https://workflowhub.eu/workflows/2024?version=3, https://workflowhub.eu/workflows/53?version=1, https://workflowhub.eu/workflows/624?version=1 |
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 |
|
terrabyte_ogc_api_processes |
terrabyte_ogc_api_processes |
txt |
This tool is a wrapper for OGC API Processes (OTB) coming from terrabyte (https://docs.terrabyte.lrz.de/). |
2024-11-11 |
https://github.com/AquaINFRA/galaxy |
0.1.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/AquaINFRA/tools-ecology/tree/terrabyte_ogc_api_process |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/terrabyte_ogc_api_processes |
|
|
|
|
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 |
2 |
2 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
2 |
2 |
|
|
True |
False |
|
trimns |
trimns |
fasta |
TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline |
2021-01-29 |
https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs |
0.1.0 |
trimns_vgp |
1.0 |
To update |
Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs |
|
|
|
|
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 |
1 |
0 |
25 |
25 |
49 |
49 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
49 |
49 |
25 |
25 |
|
|
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 |
0 |
5 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
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 |
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 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
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 |
|
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 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
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=2b1cdf79e8df5a78, 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 |
|
verkko |
verkko |
fasta, tabular, gfa1, fasta.gz |
Telomere-to-telomere assembly pipeline |
2023-01-24 |
https://github.com/marbl/verkko |
1.3.1 |
verkko |
2.3.2 |
To update |
Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko |
|
|
|
|
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 |
0 |
1 |
0 |
43 |
43 |
105 |
105 |
0 |
0 |
0 |
0 |
13 |
13 |
136 |
136 |
0 |
0 |
0 |
0 |
241 |
241 |
56 |
56 |
|
|
True |
False |
|
vigiechiro |
vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid |
tabular, html |
Tools created by the vigiechiro team to analyses and identify chiro sounds files. |
2019-03-13 |
https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro |
0.1.1 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro |
|
|
|
|
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 |
0 |
4 |
4 |
258 |
284 |
14141 |
17115 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
17115 |
14141 |
284 |
258 |
https://usegalaxy.eu/published/workflow?id=596b073ab7249aa2, https://usegalaxy.eu/published/workflow?id=c0888e0a0fb53ed3 |
|
True |
False |
|
yahs |
yahs |
agp, fasta, txt |
Yet Another Hi-C scaffolding tool |
2022-06-28 |
https://github.com/c-zhou/yahs |
1.2a.2 |
yahs |
1.2.2 |
To update |
Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs |
|
|
|
|
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
291 |
291 |
2516 |
2516 |
107 |
107 |
750 |
750 |
41 |
41 |
1062 |
1062 |
0 |
0 |
0 |
0 |
4328 |
4328 |
439 |
439 |
https://usegalaxy.eu/published/workflow?id=069d99391a69baf4, https://usegalaxy.eu/published/workflow?id=07c92110c3fffcf8, https://usegalaxy.eu/published/workflow?id=082bfd9b36e921e8, https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920, https://usegalaxy.eu/published/workflow?id=0cf3c2114ab65858, https://usegalaxy.eu/published/workflow?id=3010ecad1a342331, https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f, https://usegalaxy.eu/published/workflow?id=3b57fc81001667b5, https://usegalaxy.eu/published/workflow?id=44c92c04f1d14631, https://usegalaxy.eu/published/workflow?id=4949751217c0e211, https://usegalaxy.eu/published/workflow?id=5395e76fa828c343, https://usegalaxy.eu/published/workflow?id=652433160b04b232, https://usegalaxy.eu/published/workflow?id=792b24fc23bd3071, https://usegalaxy.eu/published/workflow?id=7b4a9aebb09b51ca, https://usegalaxy.eu/published/workflow?id=7e383fe34031a9d0, https://usegalaxy.eu/published/workflow?id=7e68cf8a67efa8e9, 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https://usegalaxy.org/published/workflow?id=325783f21bc5fef6, https://usegalaxy.org/published/workflow?id=349f1bcdbc84045f, https://usegalaxy.org/published/workflow?id=3a92253f57e553bd, https://usegalaxy.org/published/workflow?id=3b0d42747f598f82, https://usegalaxy.org/published/workflow?id=3d805d7e0f34c727, https://usegalaxy.org/published/workflow?id=3db51822f04f4ff7, https://usegalaxy.org/published/workflow?id=49a07807fcea8158, https://usegalaxy.org/published/workflow?id=6341c384ceaf47ed, https://usegalaxy.org/published/workflow?id=74049914e4a6c791, https://usegalaxy.org/published/workflow?id=7b8ee08ba291d231, https://usegalaxy.org/published/workflow?id=7fd68212ce020e6a, https://usegalaxy.org/published/workflow?id=88327cb2e0fe3c25, https://usegalaxy.org/published/workflow?id=903e35b62946ed76, https://usegalaxy.org/published/workflow?id=91a4daecbb97d03e, https://usegalaxy.org/published/workflow?id=9f4c4038d1c519e2, https://usegalaxy.org/published/workflow?id=a4a6d6846c1692f9, https://usegalaxy.org/published/workflow?id=a8cd62e1924a64e1, https://usegalaxy.org/published/workflow?id=afa89bb0e8966753, https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://usegalaxy.org/published/workflow?id=c95e9116e4b7982b, https://usegalaxy.org/published/workflow?id=f09033420c6267ab, https://usegalaxy.org/published/workflow?id=fa36d9b50e956917, https://usegalaxy.org/published/workflow?id=fb98ef955b3dbd4b, https://workflowhub.eu/workflows/1054?version=1, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/625?version=29, https://workflowhub.eu/workflows/702?version=1 |
assembly/vgp_genome_assembly |
True |
False |
|
zoo_project_ogc_api_processes |
zoo_project_ogc_api_processes |
txt |
This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. |
2024-05-03 |
https://github.com/AquaINFRA/galaxy |
0.1.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes |
|
|
|
|
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 |
5 |
5 |
28 |
28 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
28 |
28 |
5 |
5 |
https://usegalaxy.eu/published/workflow?id=e95bfab07fdec632 |
|
True |
False |