Expand Galaxy wrapper id Galaxy wrapper version Conda version Conda id Status bio.tool id bio.tool name EDAM operation EDAM topic Description bio.tool description biii Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source
askor 0.2 3.58.1 bioconductor-limma To update AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor
baric_archive 1.1.0 To update A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive
braker 2.1.6 To update BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker
braker3 3.0.8 To update BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker
feelnc2asko 0.1 1.7.8 perl-bioperl To update Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko
gcms2isocor 0.1.0 openjdk To update Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor genouest
get_pairs 0.3 python To update Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs
helixer 0.3.2 To update Gene calling with Deep Neural Networks To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer
logol 1.7.8 1.7.8 logol Up-to-date Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol
meneco 1.5.2 1.5.2 meneco Up-to-date Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco
miranda2asko 0.2 perl To update Converts miRanda output into AskOmics format To update Convert Formats miranda2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko
openlabcds2csv 0.1.0 openjdk To update Creates a summary of several "Internal Standard Report" OpenLabCDS results. To update Metabolomics openlabcds2csv genouest
peptimapper 2.0 To update Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest
Ensembl-REST 0.1.2 requests To update A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST
GAFA 0.3.1 To update Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/
TreeBest 1.9.2.post0 1.9.2.post1 treebest To update TreeBeST best To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest
apoc 1.0+galaxy1 1b16 apoc To update Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/
blast_parser 0.1.2 To update Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser
ete 3.1.2 3.1.1 ete3 To update Analyse phylogenetic trees using the ETE Toolkit To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete
export_to_cluster 0.0.2 EXPORT_DIR_PREFIX To update Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/
gblocks 0.91b 0.91b gblocks Up-to-date Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks
gstf_preparation 0.4.3 python To update GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation
hcluster_sg 0.5.1 hcluster_sg To update Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg
hcluster_sg_parser 0.2.1 To update Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser
lotus2 2.32 2.32 lotus2 Up-to-date lotus2 lotus2 Sequence feature detection Metagenomics LotuS2 OTU processing pipeline 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. Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2
miranda 3.3a+galaxy1 3.3a miranda To update Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda
plotheatmap 1.0 1.64.0 bioconductor-preprocesscore To update This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap
rdock 1.0 2013.1 rDock To update Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/
replace_chromosome_names 0.1 python To update Replace chromosome names To update Text Manipulation replace_chromosome_names earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/
rsat_filter_snps 0.1 To update Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps
smart_domains 0.1.0 1.7.8 perl-bioperl To update SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains
smina 1.0 2017.11.9 smina To update smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/
t_coffee t-coffee To update T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee
abacas 1.1 3.23 mummer To update Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas
assemblystats 1.1.0 1.7.8 perl-bioperl To update Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools
bam2mappingstats 1.1.0 perl To update Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools
bamclipper 1.0.0 1.0.0 bamclipper Up-to-date Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper nml https://github.com/tommyau/bamclipper
biohansel 2.4.0 2.6.1 bio_hansel To update Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel
biohansel_bionumeric_converter 0.2.0 pandas To update Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter nml
bundle_collections 1.3.0 2.54 perl-getopt-long To update Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections nml
collapse_collection 5.1.0 gawk To update Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections nml
combineJSON 0.1 To update JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json nml
combine_assembly_stats 1.0 2.54 perl-getopt-long To update Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools
combine_tabular_collection 0.1 To update Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection nml
concat_paired 0.2 To update Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired nml https://github.com/phac-nml/concat
cryptogenotyper 1.0 1.0 cryptogenotyper Up-to-date CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper nml https://github.com/phac-nml/CryptoGenotyper
csvtk 0.20.0 0.29.0 csvtk To update Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk nml https://github.com/shenwei356/csvtk
ectyper 1.0.0 1.0.0 ectyper Up-to-date EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper nml https://github.com/phac-nml/ecoli_serotyping
fasta2bed 1.0.0 1.7.8 perl-bioperl To update Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed nml https://github.com/phac-nml/galaxy_tools
fasta_extract 1.1.0 1.7.8 perl-bioperl To update extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract
fastqc_stats 1.2 1.7.8 perl-bioperl To update Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats nml https://github.com/phac-nml/galaxy_tools
feht 0.1.0 1.1.0 feht To update Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht nml https://github.com/phac-nml/galaxy_tools
filter_spades_repeats 1.0.1 1.7.8 perl-bioperl To update Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/
getmlst 0.2.0 srst2 To update Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml
gnali 1.1.0 1.1.0 gnali Up-to-date A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali nml https://github.com/phac-nml/gnali/
hivtrace 1.0.1 1.5.0 hivtrace To update An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace
kaptive 0.3.0 2.0.6 kaptive To update Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive nml
kat_filter 2.3 2.4.2 kat To update Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter nml
kat_sect 2.3 2.4.2 kat To update SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect nml
mauve_contig_mover 1.0.10 2.4.0.r4736 mauve To update Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover nml https://github.com/phac-nml/mauve_contig_mover
mob_suite 3.0.3 3.1.8 mob_suite To update MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite nml https://github.com/phac-nml/mob-suite
mrbayes 1.0.2 3.2.7 mrbayes To update A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml
mykrobe_parser r-base To update RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser nml https://github.com/phac-nml/mykrobe-parser
pangolin 1.1.14 4.3 pangolin To update Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin nml https://github.com/hCoV-2019/pangolin
patrist 0.1.2 python To update Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist nml https://github.com/phac-nml/patrist
plasmid_profiler 0.1.6 r To update Explores plasmid content in WGS data To update plasmid_profiler nml
plasmid_profiler_suite To update Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler nml
plasmidspades 1.1 3.15.5 spades To update Genome assembler for assemblying plasmid To update Assembly plasmidspades nml
pneumocat 1.2.1 1.2.1 pneumocat Up-to-date Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat nml https://github.com/phe-bioinformatics/PneumoCaT
promer 1.2 python To update Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer
pseudogenome 1.0.0 1.7.8 perl-bioperl To update Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome nml
quasitools 0.7.0 0.7.0 quasitools Up-to-date A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools nml https://github.com/phac-nml/quasitools
refseq_masher 0.1.2 0.1.2 refseq_masher Up-to-date Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher nml https://github.com/phac-nml/refseq_masher
seqtk_nml 1.0.1 1.4 seqtk To update Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml nml https://github.com/phac-nml/snvphyl-galaxy
sistr_cmd 1.1.1 1.1.1 sistr_cmd Up-to-date SISTR in silico serotyping tool Up-to-date https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd nml
smalt 0.7.6 0.7.6 smalt Up-to-date SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt nml https://sourceforge.net/projects/smalt/
spades_header_fixer 1.1.2+galaxy1 sed To update Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer nml https://github.com/phac-nml/galaxy_tools
spatyper 0.3.3 0.3.3 spatyper Up-to-date Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper
spolpred 1.0.1 spolpred To update A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred nml
srst2 0.3.7 0.2.0 srst2 To update Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml
staramr 0.10.0 0.10.0 staramr Up-to-date Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr
stringmlst 1.1.0 0.6.3 stringMLST To update Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml
tree_relabeler 1.1.0 1.7.8 perl-bioperl To update Relabels the tips of a newick formatted tree. To update Text Manipulation tree_relabeler nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler
wade 0.2.5+galaxy1 0.2.6 wade To update identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade nml https://github.com/phac-nml/wade
camera 1.48.0 0.4_1 r-snow To update To update Metabolomics camera workflow4metabolomics
correlation_analysis 1.0.1+galaxy0 1.1_4 r-batch To update [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/
genform r8 genform To update genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/
influx_data_manager 1.0.0 1.0.0 influx-si-data-manager Up-to-date Handling influx_si data inputs in Galaxy workflows Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager
influx_si 7.0.1 7.0.2 influx_si To update metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/
ipo 1.10.0 1.28.0 bioconductor-ipo To update [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo lecorguille https://github.com/rietho/IPO
isoplot 1.3.0+galaxy1 1.3.1 isoplot To update Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main
kmd_hmdb_data_plot 1.0.0 python To update retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/
mixmodel4repeated_measures 3.1.0 r-lme4 To update [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics
ms2snoop 2.2.1 r-base To update [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop workflow4metabolomics
nmr_annotation 3.0.0 1.1_4 r-batch To update [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation
nmr_annotation2d 2.0.0 1.1_4 r-batch To update [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics
nmr_preprocessing 1.1_4 r-batch To update [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing
normalization 1.0.7 1.1_4 r-batch To update [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization
physiofit 3.3.2 3.3.2 physiofit Up-to-date PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes Up-to-date physiofit.readthedocs.io Metabolomics physiofit workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit
physiofit_manager 1.0.1 1.0.1 physiofit_data_manager Up-to-date Handling of physiofit input files Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager Metabolomics physiofit_manager workflow4metabolomics
xcms 3.12.0 4.0.0 bioconductor-xcms To update To update https://github.com/sneumann/xcms Metabolomics xcms workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/
apollo 4.2.13 apollo To update Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo
askomics 0.5 askocli To update Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics
chado 2.3.9 python-chado To update Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado
genenotebook 0.4.13 0.4.13 genoboo Up-to-date Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io Up-to-date https://genenotebook.github.io Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook
jbrowse python To update A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse
repeatexplorer2 2.3.8 To update Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2
tripal 3.2.1 python-tripal To update Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal To update https://github.com/galaxy-genome-annotation/python-tripal Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal
w4mcorcov 0.98.18 r-base To update OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master
w4mclassfilter 0.98.19 r-base To update Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master
w4mjoinpn 0.98.2 8.25 coreutils To update Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master
2d_auto_threshold 0.0.5-2 scikit-image To update scikit-image scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Automatic thresholding Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image To update https://github.com/bmcv Imaging 2d_auto_threshold imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/
2d_feature_extraction 0.1.1-2 pandas To update scikit-image scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 2D feature extraction Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image To update https://github.com/bmcv Imaging 2d_feature_extraction imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/
2d_filter_segmentation_by_features 0.0.1-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics filter segmentation by rules Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/
2d_histogram_equalization 0.0.1-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics 2d histogram equalization Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging 2d_histogram_equalization imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/
2d_simple_filter 0.0.3-3 scikit-image To update scikit-image scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 2d simple filter Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image To update https://github.com/bmcv Imaging 2d_simple_filter imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/
3d_tensor_feature_dimension_reduction 0.0.1 numpy To update Dimensionality reduction for features (channels) of 3D tensor data using UMAP To update https://github.com/BMCV/galaxy-image-analysis Imaging 3d_tensor_feature_dimension_reduction imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/
anisotropic_diffusion 0.2-2 scikit-image To update Anisotropic image diffusion To update https://github.com/bmcv Imaging anisotropic_diffusion imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/
bfconvert 6.7.0+galaxy2 6.7.0 bftools To update Convert image python-bioformats To update https://github.com/bmcv Imaging, Convert Formats bfconvert imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/
binary2labelimage 0.5 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Binary 2 label image Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging binary2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/
binaryimage2points 0.1-2 numpy To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Binary Image to Points Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging binaryimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/
bioformats2raw 0.7.0 To update Convert image to OME-Zarr To update https://github.com/Euro-BioImaging Imaging, Convert Formats bioformats2raw imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw
color-deconvolution 0.8-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Color-deconvolution methods Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging color_deconvolution imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/
concat_channels 0.2-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Concatenate images Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging concat_channels imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/
coordinates_of_roi 0.0.4-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Coordinates of ROI Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging coordinates_of_roi imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/
count_objects 0.0.5-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Count Objects Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging count_objects imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/
curl_post 0.0.2 curl To update Send file via cURL POST To update https://github.com/bmcv Data Export, Web Services curl_post imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post
curve_fitting 0.0.3-2 numpy To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Polynomial curve fitting to data points Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/
detection_viz 0.3-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Detection Visualization Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging detection_viz imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/
image_info 5.7.1 6.7.0 bftools To update Extracts image metadata python-bioformats To update https://github.com/bmcv Imaging image_info imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/
image_registration_affine 0.0.3-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Intensity-based Image Registration Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging image_registration_affine imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/
imagecoordinates_flipaxis 0.1-2 pandas To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Flip coordinate axes Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging imagecoordinates_flipaxis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/
labelimage2points 0.2-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Label Image to Points Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging labelimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/
landmark_registration 0.1.0-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Landmark Registration Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging landmark_registration imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/
mahotas-features 0.7-2 mahotas To update Compute image features using mahotas. mahotas-feature-computation To update https://github.com/luispedro/mahotas Imaging mahotas_features imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/
mergeneighboursinlabelimage 0.3-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Merge Neighbours in Label Image Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging mergeneighboursinlabelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage
overlay_images 0.0.4 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Overlay two images Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/
permutate_axis 0.2-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Permutates axes Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging permutate_axis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/
points2binaryimage 0.2-1 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Points to Binary Image Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging points2binaryimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/
points2labelimage 0.3-2 numpy To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Points to label image Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging points2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/
points_association_nn 0.0.3-2 numpy To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Association of points in consecutive frames Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/
projective_transformation 0.1.2-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Projective transformation Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging projective_transformation imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/
projective_transformation_points 0.1.1-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Projective transformation of ROIs defined by pixel (point) coordinates Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging projective_transformation_points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/
rfove 2023.11.12 To update rfove RFOVE Image analysis Cell biology, Biomedical science, Imaging Perform segmentation region-based fitting of overlapping ellipses RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. To update https://sites.google.com/site/costaspanagiotakis/research/cs Imaging rfove imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/
scale_image 0.4-2 pillow To update scikit-image scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Scale image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image To update https://github.com/bmcv Imaging scale_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/
segmetrics 1.4 1.4.1 segmetrics To update segmetrics SegMetrics Image analysis Image segmentation and object detection performance measures Image segmentation and object detection performance measures segmetrics To update https://github.com/bmcv Imaging segmetrics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/
slice_image 0.3-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Slice image Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging slice_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/
split_labelmap 0.2-2 scikit-image To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Split Labelmaps Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/bmcv Imaging split_labelmap imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/
spot_detection_2d 0.0.3-2 imageio To update galaxy_image_analysis Galaxy Image Analysis Image analysis Imaging, Bioinformatics Spot detection in 2D image sequence Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/
superdsm 0.2.0 0.2.0 superdsm Up-to-date superdsm SuperDSM Image analysis Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. superdsm Up-to-date https://github.com/bmcv Imaging superdsm imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/
unzip 6.0 unzip To update Unzip file To update https://github.com/bmcv Convert Formats unzip imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/
visceral-evaluatesegmentation 0.5-2 2015.07.03 visceral-evaluatesegmentation To update Visceral Project - Evaluate Segmentation Tool evaluatesegmentation-tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation
wsi_extract_top_view 0.2-2 scikit-image To update WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/
add_value 1.0.1 perl To update Add a value as a new column. To update Text Manipulation add_value devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value
annotation_profiler 1.0.0 0.11.0 bx-python To update Profile Annotations for a set of genomic intervals To update Genomic Interval Operations annotation_profiler devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler
best_regression_subsets 1.0.0 numpy To update Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets
blat_coverage_report 1.0.0 To update Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report
blat_mapping 1.0.0 To update Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping
bowtie_wrappers 1.2.0 1.3.1 bowtie To update Galaxy wrappers for the Bowtie short read mapping tools. To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers bowtie_wrappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers
canonical_correlation_analysis 1.0.0 R To update Canonical Correlation Analysis To update Statistics canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis
categorize_elements_satisfying_criteria 1.0.0 To update Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria
ccat 0.0.2 3.0 ccat To update Control-based ChIP-seq Analysis Tool To update ChIP-seq ccat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat
cd_hit_dup 0.0.1 4.8.1 cd-hit-auxtools To update simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup
change_case 1.0.1 perl To update Convert column case. To update Text Manipulation change_case devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case
compute_motif_frequencies_for_all_motifs 1.0.0 To update Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs
compute_motifs_frequency 1.0.0 To update Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency
compute_q_values 1.0.1 R To update Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values
condense_characters 1.0.0 To update Condense consecutive characters. To update Text Manipulation condense_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters
convert_characters 1.0.1 python To update Convert delimiters to tab. To update Text Manipulation convert_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters
convert_solid_color2nuc 1.0.0 To update Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc
correlation 1.0.0 rpy To update Correlation for numeric columns To update Statistics correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation
count_gff_features 0.2 1.1.0 galaxy-ops To update Count GFF Features To update Sequence Analysis count_gff_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features
ctd_batch 1.0.0 To update CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch
cummerbund 2.16.0 fonts-conda-ecosystem To update Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund
cummerbund_to_tabular 1.0.1 To update Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. To update Convert Formats, Next Gen Mappers cummerbund_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular
cut_columns 1.0.2 To update Select columns from a dataset. To update Text Manipulation cut_columns devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns
delete_overlapping_indels 1.0.0 To update Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels
dgidb_annotator 0.1 To update Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) To update Systems Biology, Variant Analysis dgidb_annotator devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator
divide_pg_snp 1.0.0 To update Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp
draw_stacked_barplots 1.0.0 R To update Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots
dwt_cor_ava_perclass 1.0.1 1.7.5 r-waveslim To update Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass
dwt_cor_avb_all 1.0.1 1.7.5 r-waveslim To update Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all
dwt_ivc_all 1.0.1 1.7.5 r-waveslim To update Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all
dwt_var_perclass 1.0.1 1.7.5 r-waveslim To update Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass
dwt_var_perfeature 1.0.2 r-bitops To update Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature
express 1.1.1 1.5.1 eXpress To update Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express
fasta_compute_length 1.0.3 python To update Compute sequence length To update Fasta Manipulation fasta_compute_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length
fasta_concatenate_by_species 0.0.1 0.11.0 bx-python To update Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species
fasta_filter_by_length 1.2 python To update Filter sequences by length To update Fasta Manipulation fasta_filter_by_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length
fasta_to_tabular 1.1.1 python To update FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular
fastq_trimmer_by_quality 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date FASTQ Quality Trimmer by sliding window Up-to-date Fastq Manipulation fastq_trimmer_by_quality devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality
fastqsolexa_to_fasta_qual 1.0.0 To update FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual
featurecounter 2.0.0 0.11.0 bx-python To update Feature coverage To update Sequence Analysis, Variant Analysis featurecounter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter
filter_transcripts_via_tracking 0.1 To update Filter Combined Transcripts To update RNA filter_transcripts_via_tracking devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking
generate_pc_lda_matrix 1.0.0 To update Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix
getindelrates_3way 1.0.0 0.11.0 bx-python To update Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way
getindels_2way 1.0.0 numpy To update Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way
gmaj 2.0.1 To update GMAJ Multiple Alignment Viewer To update Visualization gmaj devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj
hisat 1.0.3 hisat To update HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat
histogram 1.0.4 2.7.8 rpy2 To update Histogram of a numeric column To update Graphics, Statistics histogram devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram
indels_3way 1.0.3 To update Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way
kernel_canonical_correlation_analysis 1.0.0 rpy To update Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis
kernel_principal_component_analysis 1.0.0 rpy To update Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis
lastz_paired_reads 1.1.1 1.04.22 lastz To update Galaxy wrapper for the Lastz alignment tool on paired reads To update Next Gen Mappers lastz_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads
lda_analysis 1.0.1 R To update Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis
linear_regression 1.0.1 R To update Perform Linear Regression To update Statistics linear_regression devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression
logistic_regression_vif 1.0.1 numpy To update Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif
maf_cpg_filter 1.0.0 0.11.0 bx-python To update Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter
mapping_to_ucsc 1.0.0 To update Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc
megablast_xml_parser 1.0.1 python To update Parse blast XML output To update Next Gen Mappers, Convert Formats megablast_xml_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser
merge_cols 1.0.3 python To update Merge columns together. To update Text Manipulation merge_cols devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols
microsatellite_birthdeath 1.0.0 To update Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath
microsats_alignment_level 1.0.0 sputnik To update Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level
microsats_mutability 1.1.0 0.11.0 bx-python To update Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability
mine 0.0.1 MINE To update Maximal Information-based Nonparametric Exploration To update Variant Analysis mine devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine
multispecies_orthologous_microsats 1.0.0 bx-sputnik To update Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats
mutate_snp_codon 1.0.0 To update Mutate Codons with SNPs To update Variant Analysis mutate_snp_codon devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon
partialr_square 1.0.0 R To update Compute partial R square To update Statistics partialr_square devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square
pearson_correlation 1.0.0 To update Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation
pgsnp2gd_snp 1.0.0 To update Convert from pgSnp to gd_snp To update Variant Analysis pgsnp2gd_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp
pileup_interval 1.0.3 0.11.0 bx-python To update Pileup-to-Interval condenses pileup format into ranges of bases To update SAM pileup_interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval
pileup_parser 1.0.2 perl To update Filter pileup on coverage and SNPs To update https://github.com/galaxyproject/tools-devteam/ SAM pileup_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser
plot_from_lda 1.0.1 R To update Draw ROC plot on "Perform LDA" output To update Graphics, Statistics plot_from_lda devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda
principal_component_analysis 1.0.2 rpy To update Principal Component Analysis To update Statistics principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis
quality_filter 1.0.1 0.11.0 bx-python To update Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter
rcve 1.0.0 R To update Compute RCVE To update Sequence Analysis, Variant Analysis rcve devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve
remove_beginning 1.0.0 To update Remove lines from the beginning of a file. To update Text Manipulation remove_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning
rmap 1.0.0 2.1 rmap To update RMAP for Solexa Short Reads Alignment To update Next Gen Mappers rmap devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap
rmapq 1.0.0 2.1 rmap To update RMAPQ for Solexa Short Reads Alignment with Quality Scores To update Next Gen Mappers rmapq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq
sam2interval 1.0.2 python To update Convert SAM to interval. To update SAM sam2interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval
sam_bitwise_flag_filter 1.0.1 python To update Filter SAM on bitwise flag values To update SAM sam_bitwise_flag_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter
scatterplot 1.0.3 numpy To update Scatterplot of two numeric columns To update Graphics, Statistics scatterplot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot
short_reads_figure_high_quality_length 1.0.0 rpy To update Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length
short_reads_figure_score 1.0.2 fontconfig To update Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score
short_reads_trim_seq 1.0.0 To update Select high quality segments To update Fastq Manipulation short_reads_trim_seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq
show_beginning 1.0.0 To update Select lines from the beginning of a file. To update Text Manipulation show_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning
show_tail 1.0.0 To update Select lines from the end of a file. To update Text Manipulation show_tail devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail
sicer 1.1 1.1 SICER Up-to-date Statistical approach for the Identification of ChIP-Enriched Regions Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq sicer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer
split_paired_reads 1.0.0 To update Split paired end reads To update Fastq Manipulation split_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads
substitution_rates 1.0.0 To update Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates
substitutions 1.0.1 0.11.0 bx-python To update Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions
t_test_two_samples 1.0.1 R To update T Test for Two Samples To update Statistics t_test_two_samples devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples
table_annovar 0.2 annovar To update Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered To update Variant Analysis table_annovar devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar
tabular_to_fasta 1.1.1 python To update Tabular-to-FASTA To update Convert Formats tabular_to_fasta devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta
tophat 1.5.0 1.19.2 samtools To update Tophat for Illumina To update RNA, Next Gen Mappers tophat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat
tophat2 2.1.1 2.5.3 bowtie2 To update Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2
tophat_fusion_post 0.1 blast+ To update Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post
trimmer 0.0.1 To update Trim leading or trailing characters. To update Text Manipulation trimmer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer
ucsc_custom_track 1.0.1 python To update Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track
varscan_version_2 2.4.2 2.4.6 varscan To update VarScan wrapper To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan_version_2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2
vcf2pgsnp 1.0.0 To update VCF to pgSnp To update Variant Analysis vcf2pgsnp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp
vcf_annotate 1.0.0 To update Annotate a VCF file (dbSNP, hapmap) To update Variant Analysis vcf_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate
vcf_extract 1.0.0 To update Extract reads from a specified region To update Variant Analysis vcf_extract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract
vcf_filter 1.0.0 To update Filter a VCF file To update Variant Analysis vcf_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter
vcf_intersect 1.0.0 To update Generate the intersection of two VCF files To update Variant Analysis vcf_intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect
weightedaverage 1.0.1 1.1.0 galaxy-ops To update Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage
windowsplitter 1.0.1 0.11.0 bx-python To update Make windows To update Sequence Analysis, Variant Analysis windowsplitter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter
xy_plot 1.0.2 r-base To update Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot
basecoverage 1.0.0 0.11.0 bx-python To update Base Coverage of all intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations basecoverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage
cluster 1.0.0 0.11.0 bx-python To update Cluster the intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations cluster devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster
complement 1.0.0 0.11.0 bx-python To update Complement intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations complement devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement
concat 1.0.1 0.11.0 bx-python To update Concatenate two bed files To update https://github.com/galaxyproject/gops Genomic Interval Operations concat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat
coverage 1.0.0 0.11.0 bx-python To update Coverage of a set of intervals on second set of intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations coverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage
flanking_features 4.0.1 0.11.0 bx-python To update Fetch closest non-overlapping feature for every interval To update https://github.com/galaxyproject/gops Genomic Interval Operations flanking_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features
get_flanks 1.0.0 0.11.0 bx-python To update Get flanks returns flanking region/s for every gene To update https://github.com/galaxyproject/gops Genomic Interval Operations get_flanks devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks
intersect 1.0.0 0.11.0 bx-python To update Intersect the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect
join 1.0.0 0.11.0 bx-python To update Join the intervals of two datasets side-by-side To update https://github.com/galaxyproject/gops Genomic Interval Operations join devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join
merge 1.0.0 0.11.0 bx-python To update Merge the overlapping intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge
subtract 1.0.0 0.11.0 bx-python To update Subtract the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract
subtract_query 0.1 0.11.0 bx-python To update Subtract Whole Dataset from another dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract_query devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query
tables_arithmetic_operations 1.0.0 perl To update Arithmetic Operations on tables To update https://github.com/galaxyproject/gops Genomic Interval Operations tables_arithmetic_operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations
hgv_fundo 1.0.0 To update FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo
hgv_hilbertvis 1.0.0 R To update HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis
snpfreq 1.0.1 R To update snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq
find_diag_hits 1.0.0 0.10.0 taxonomy To update Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits
gi2taxonomy 1.1.1 0.10.0 taxonomy To update Fetch taxonomic representation To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy
kraken2tax 1.2+galaxy0 gawk To update Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/
lca_wrapper 1.0.1 0.10.0 taxonomy To update Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper
poisson2test 1.0.0 0.10.0 taxonomy To update Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test
t2ps 1.0.0 0.10.0 taxonomy To update Draw phylogeny To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps
t2t_report 1.0.0 0.10.0 taxonomy To update Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report
vcftools_annotate 0.1 echo To update Annotate VCF using custom/user-defined annotations To update https://vcftools.github.io/ Variant Analysis vcftools_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate
vcftools_compare 0.1 1.11 tabix To update Compare VCF files to get overlap and uniqueness statistics To update https://vcftools.github.io/ Variant Analysis vcftools_compare devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare
vcftools_consensus 0.1.11 1.19.2 samtools To update Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus
vcftools_isec 0.1.1 1.11 tabix To update Intersect multiple VCF datasets To update https://vcftools.github.io/ Variant Analysis vcftools_isec devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec
vcftools_merge 0.1.11 1.11 tabix To update Merge multiple VCF datasets into a single dataset To update https://vcftools.github.io/ Variant Analysis vcftools_merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge
vcftools_slice 0.1 echo To update Subset VCF dataset by genomic regions To update https://vcftools.github.io/ Variant Analysis vcftools_slice devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice
vcftools_subset 0.1 1.11 tabix To update Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset
10x_bamtofastq 1.4.1 1.4.1 10x_bamtofastq Up-to-date Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq
AggregateAlignments 0.6.0 0.6.0 graphclust-wrappers Up-to-date Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments
AlignCluster 0.1 0.6.0 graphclust-wrappers To update Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster
CMFinder 0.4 0.6.0 graphclust-wrappers To update Determines consensus motives for sequences. To update RNA graphclust_cmfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder
CollectResults 0.5 0.6.0 graphclust-wrappers To update Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults
CollectResultsNoAlign 0.5 0.6.0 graphclust-wrappers To update Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign
GSPAN 0.4 0.6.0 graphclust-wrappers To update Second step of GraphClust To update RNA graphclust_fasta_to_gspan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN
LocARNAGraphClust 0.4 0.6.0 graphclust-wrappers To update MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust
NSPDK 0.6.0 graphclust-wrappers To update Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK
Plotting 0.4 seaborn To update Plotting results for GraphClust To update RNA graphclust_motif_finder_plot rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting
PrepareForMlocarna 0.4 0.6.0 graphclust-wrappers To update This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna
Preprocessing 0.5 0.6.0 graphclust-wrappers To update Preprocessing input for GraphClust To update RNA graphclust_preprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust
Structure_GSPAN 0.4 0.6.0 graphclust-wrappers To update Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN
agat 1.2.0 1.3.0 agat To update agat AGAT Data handling, Genome annotation Genomics GTF/GFF analysis toolkit Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat
antismash 6.1.1 7.1.0 antismash To update antismash antiSMASH Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. To update https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash
atactk_trim_adapters 0.1.6 0.1.9 atactk To update Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters
augustus 3.1.0 3.5.0 augustus To update AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus
bamhash 1.1 1.1 bamhash Up-to-date Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash
barcode_collapse 0.1.0 0.22.0 pysam To update Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse
bigwig_to_bedgraph 0.1.0 ucsc_tools To update Convert from bigWig to bedGraph format To update Convert Formats bigwig_to_bedgraph bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph
biomodelsML 1 To update Random Forest model to predict efficacy of immune checkpoint blockade across multiple cancer patient cohorts To update https://www.ebi.ac.uk/biomodels/BIOMD0000001066 Machine Learning biomodels_biomd0000001066 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML
bionano 3.7.0 To update Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano
bismark 0.22.1 0.24.2 bismark To update A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark
blobtoolkit 4.0.7 To update Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit
blockbuster 0.1.2 blockbuster To update Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster
canu 2.2 2.2 canu Up-to-date canu CANU De-novo assembly Genomics Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. Up-to-date https://github.com/marbl/canu canu bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu
cellpose 3.0.1 To update Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose
cellprofiler To update CellProfiler CellProfiler Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype cellProfiler wrapper Tool for quantifying data from biological images, particularly in high-throughput experiments. cellprofiler To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools
cellprofiler_v4 4.2.6 To update cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools
chipseeker 1.32.0 1.38.0 bioconductor-chipseeker To update A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker
circexplorer 1.1.10 circexplorer To update A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer
combine_metaphlan_humann 0.3.0 python To update combine_metaphlan_and_humann Combine Metaphlan and HUMAnN Aggregation Metagenomics, Molecular interactions, pathways and networks Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances "This tool combine MetaPhlAn outputs and HUMANnN outputs." - Galaxy tool wrapper To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2
compare_humann2_output 0.2.0 To update compare_humann2_outputs Compare HUMAnN2 outputs Comparison Metagenomics, Gene and protein families Compare outputs of HUMAnN2 for several samples and extract similar and specific information "This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples." - Galaxy tool wrapper To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output
cpat 3.0.5 3.0.5 cpat Up-to-date Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat
crt 1.2.0 1.2 crisper_recognition_tool To update CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt
diff 3.7 diffutils To update GNU diff tool that calculates the differences between two files. To update http://www.gnu.org/software/diffutils/ Text Manipulation diff bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff
diffbind To update Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind
edta 2.2.0 edta To update edta The Extensive de novo TE Annotator (EDTA) De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. To update https://github.com/oushujun/EDTA Variant Analysis edta bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta
epicseg @VERSION_STRING@ 1.0 epicseg To update EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg
fastq_info 0.25.1 0.25.2 fastq_utils To update FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info
file_manipulation 0.4 python To update This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation
find_subsequences 0.3 1.70 biopython To update To update find_subsequences bgruening
flye 2.9.3 2.9.3 flye Up-to-date Assembly of long and error-prone reads. Up-to-date https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye
footprint 1.0.0 1.0.1 footprint To update Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint
format_cd_hit_output 1.0.0+galaxy1 To update Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/
format_metaphlan2_output 0.2.0 To update format_metaphlan2_output Format metaphlan2 output Formatting Taxonomy, Metagenomics Format MetaPhlAn2 output to extract abundance at different taxonomic levels "This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains)." - Galaxy tool wrapper To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/
gfastats 1.3.6 1.3.6 gfastats Up-to-date gfastats gfastats Data handling Computational biology Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats
glimmer_hmm To update GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm
gotohscan 1.3.0 1.3 gotohscan To update Find subsequences in db To update Sequence Analysis gotohscan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan
graph_converter 0.1.0 To update Convert between different graph formats To update Convert Formats graph_converter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter
graphclust 0.1 GraphClust To update GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust
graphmap 0.5.2 0.6.3 graphmap To update Mapper for long, error-prone reads. To update https://github.com/isovic/graphmap/ Assembly graphmap bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap
hclust2 0.99 1.0.0 hclust2 To update Plots heatmaps To update https://bitbucket.org/nsegata/hclust2/ Data Visualization hclust2 rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2
hictk 0.0.8 0.0.9 hictk To update hictk, a blazing-fast toolkit to work with .hic and .cool files To update https://github.com/paulsengroup/hictk hictk bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk
hicup 0.9.2 To update The HiCUP-Pipeline from the Bioinformatics Babraham Institute. To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics hicup bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup
hifiasm 0.19.8 0.19.8 hifiasm Up-to-date A fast haplotype-resolved de novo assembler Up-to-date https://github.com/chhylp123/hifiasm Assembly hifiasm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm
homer To update Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer
illumina_methylation_analyser 0.1 Rscript To update Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser
bia-ftplinks 0.1.0 wget To update Tool to query ftp links for study from bioimage archive To update Imaging bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools
graphicsmagick 1.3.42 1.3.26 graphicsmagick To update Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/
imagej2 To update imagej ImageJ2 Image analysis, Image annotation, Visualisation Imaging ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. imagej2 To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2
woundhealing 1.6.1 1.6.1 fiji-morpholibj Up-to-date Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools
instagraal 0.1.6 To update instagraal instaGRAAL Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites Large genome reassembly based on Hi-C data Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) To update https://github.com/koszullab/instaGRAAL Assembly instagraal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal
iprscan5 To update Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5
itsx 1.1.3 1.1.3 itsx Up-to-date ITSx ITSx Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx
jupyter_job 0.0.1 To update Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job
labels labels To update remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels
lighter 1.0 1.1.2 lighter To update Lighter is a kmer-based error correction method for whole genome sequencing data To update Sequence Analysis, Fasta Manipulation lighter bgruening https://github.com/mourisl/Lighter
mafft 7.508 7.520 mafft To update MAFFT MAFFT Multiple sequence alignment Sequence analysis Multiple alignment program for amino acid or nucleotide sequences MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. To update RNA mafft rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft
mavedb 0.9 To update data source for MaveDB To update Data Source mavedb_importer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/
mcl 14.137 22.282 mcl To update Markov Cluster Algorithm To update http://micans.org/mcl/ Sequence Analysis, Metagenomics mcl bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mcl
methtools 0.1.1 methtools To update tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools
methyldackel 0.5.2 0.6.1 methyldackel To update A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel
methylkit 0.99.2 1.28.0 bioconductor-methylkit To update A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics methylkit rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit
metilene 0.2.8 metilene To update Differential DNA methylation calling To update RNA, Statistics metilene rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene
miclip 1.2.0 Rscript To update Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip
minced 0.2.0 0.4.2 minced To update MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced
minipolish 0.1.3 0.1.3 minipolish Up-to-date minipolish minipolish Localised reassembly, Read depth analysis Sequence assembly, Sequencing Polishing miniasm assemblies A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish
mitohifi 3 To update Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi
molecule2gspan 0.2 2.3.90dev7d621d9 openbabel To update converter To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats molecule_to_gspan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan
music_deconvolution 0.1.1 0.1.1 music-deconvolution Up-to-date Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/
nanopolish 0.14.0 0.14.0 nanopolish Up-to-date Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. Up-to-date https://github.com/jts/nanopolish nanopolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish
netboxr 1.6.0 1.9.0 bioconductor-netboxr To update netboxr enables automated discovery of biological process modules by network analysis To update Systems Biology netboxr bgruening
nextdenovo 2.5.0 2.5.2 nextdenovo To update nextdenovo NextDenovo De-novo assembly, Genome assembly Sequencing, Sequence assembly String graph-based de novo assembler for long reads NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo
nucleosome_prediction 3.0 3.0 nucleosome_prediction Up-to-date Prediction of Nucleosomes Positions on the Genome Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction
numeric_clustering 0.9 anaconda To update Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering
openms 2.1.0 3.1.0 openms To update OpenMS in version 2.1. To update Proteomics openms bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms
pandas_rolling_window 0.1 numpy To update Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window
peakachu 0.2.0+galaxy1 0.2.0 peakachu To update PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu rnateam https://github.com/tbischler/PEAKachu
perf 5.11.0 perf To update suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf
pfamscan 1.6 1.6 pfam_scan Up-to-date pfamscan PfamScan Protein sequence analysis Sequence analysis Search a FASTA sequence against a library of Pfam HMM. This tool is used to search a FASTA sequence against a library of Pfam HMM. Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan
pg_tools postgresql To update tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools bgruening https://github.com/bgruening/galaxytools/tools/pgtools
pharmcat To update Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat
piranha 1.2.1 piranha To update Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha
platypus 0.0.11 platypus To update efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus
plotly_ml_performance_plots 0.2 pandas To update performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots
plotly_parallel_coordinates_plot 0.2 python To update parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot
plotly_regression_performance_plots 0.1 python To update performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots
protease_prediction 0.9 2.0 eden To update This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction
protein_properties 0.2.0 1.70 biopython To update Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties
improviser To update Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser
racon 1.5.0 1.5.0 racon Up-to-date Racon Racon Genome assembly, Mapping assembly, Sequence trimming Whole genome sequencing, Sequence assembly, Plant biology Consensus module for raw de novo DNA assembly of long uncorrected reads. The Possibility to Use Oxford Nanopore Technology | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here: https://github.com/isovic/racon| Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step | Consensus module for raw de novo DNA assembly of long uncorrected reads Up-to-date https://github.com/isovic/racon Sequence Analysis racon bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon
repeat_masker 0.1.2 4.1.5 RepeatMasker To update RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker
replaceColumn 0.2 To update A tool to replace all column entries of a file given by values of a key-value file. To update Text Manipulation replace_column_by_key_value_file bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn
rest_tool 0.1.0 To update This tool fetches data from pubchem via the PubChem REST API. To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source pubchem_rest_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool
antarna 1.1 antarna To update antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/
aresite2 0.1.2 python To update AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2
blockclust 1.1.1 1.1.1 blockclust Up-to-date BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust
cmsearch_deoverlap 0.08+galaxy0 perl To update removes lower scoring overlaps from cmsearch results. To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap
cmv 1.0.8 1.0.8 cmv Up-to-date cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv
cofold 2.0.4 cofold To update Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold
compalignp 1.0 1.0 compalignp Up-to-date Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/
coprarna 2.1.1 2.1.4 coprarna To update Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna rnateam https://github.com/PatrickRWright/CopraRNA
dewseq 0.1.0+galaxy0 python To update DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq
dorina 1.0 To update data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/
dot2ct 5.7.a 6.4 rnastructure To update Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct
dotknot 1.3.1 vienna_rna To update DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot
exparna 1.0.1 1.0.1 exparna Up-to-date ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna
graphprot 1.1.7+galaxy1 1.1.7 graphprot To update GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot
htseq-clip 0.1.0+galaxy0 2.19.0b0 htseq-clip To update htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip
infernal 1.1.4 1.1.5 infernal To update infernal Infernal Nucleic acid feature detection Sequence sites, features and motifs Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. To update http://infernal.janelia.org/ RNA infernal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal
inforna To update INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna
intarna 3.4.0 3.4.0 intarna Up-to-date Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna
kinwalker To update Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker
locarna 2.0.0 locarna To update LocARNA - A suite for multiple alignment and folding of RNAs To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna
mea 0.6.4 mea To update Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea
mqc 1.9 1.10 mqc To update Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/
nastiseq 1.0 1.0 r-nastiseq Up-to-date A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq
paralyzer 1.5 1.5 paralyzer Up-to-date A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer
pipmir 0.1.0 1.1 pipmir To update A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir
rRNA 0.1 hmmsearch3.0 To update Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA
rbpbench 0.8.1 0.8.1 rbpbench Up-to-date rbpbench RBPBench RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs Up-to-date https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench
rcas 1.5.4 1.28.2 bioconductor-rcas To update RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/
reago 1.1 1.1 reago Up-to-date Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago
remurna 1.0.0 1.0 remurna To update remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna
ribotaper 1.3.1a 1.3.1 ribotaper To update ribotaper RiboTaper Gene expression profiling Functional genomics A method for defining traslated ORFs using Ribosome Profiling data. New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/
rna_shapes 3.3.0 @EXECUTABLE@ To update Compute secondary structures of RNA To update RNA rnashapes rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes
rnabob 2.2.1 rnabob To update Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob
rnacode 0.3.2 0.3 rnacode To update Analyze the protein coding potential in MSA To update RNA rnacode rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode
rnacommender 0.1.1 3.5 sam To update RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender
rnalien 1.3.6 1.8.0 rnalien To update RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien
rnasnp 1.2.0 1.2 rnasnp To update RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp
rnaz 2.1.1 2.1.1 rnaz Up-to-date RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz
selectsequencesfrommsa 1.0.5 1.0.5 selectsequencesfrommsa Up-to-date SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa
sortmerna 4.3.6 4.3.6 sortmerna Up-to-date sortmerna SortMeRNA Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Up-to-date http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna
sshmm 1.0.7 1.0.7 sshmm Up-to-date ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/
targetfinder 1.7 1.7 targetfinder Up-to-date Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/
trna_prediction 0.6 1.2.41 aragorn To update Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction
vienna_rna 2.2.10 2.6.4 viennarna To update ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna
sailfish bzip2 To update Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish
salmon 1.10.1 1.10.2 salmon To update Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon
sambamba 1.0 sambamba To update SAMBAMBA: process your BAM data faster! To update https://github.com/lomereiter/sambamba SAM sambamba rnateam https://github.com/bgruening/galaxytools/tree/master/tools/sambamba
sed 0.0.1 sed To update Manipulate your data with the sed command line tool. To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation sed_wrapper bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed
segemehl 0.3.4 segemehl To update segemehl - short read mapping with gaps To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers segemehl rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl
sklearn To update Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn
splitfasta 0.4.0 1.70 biopython To update Split a multi-sequence fasta file into files containing single sequences To update Text Manipulation splitfasta rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta
statistics 0.3 numpy To update Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics
stress_ng 0.12.04 stress-ng To update stress test a computer system in various selectable ways To update Web Services stress_ng bgruening-util https://github.com/ColinIanKing/stress-ng
tapscan 4.76+galaxy0 3.4 hmmer To update Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan
add_line_to_file 0.1.0 8.25 coreutils To update Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file
column_arrange_by_header 0.2 To update Column arrange by header name To update Text Manipulation column_arrange_by_header bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header
join_files_on_column_fuzzy 1.0.1 python To update Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy
split_file_on_column 0.6 gawk To update Split a file on a specific column. To update Text Manipulation split_file_on_column bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column
split_file_to_collection 0.5.1 python To update Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update Text Manipulation split_file_to_collection bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection
text_processing 9.3 8.25 coreutils To update High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing
tgsgapcloser 1.0.3 1.2.1 tgsgapcloser To update TGS-GapCloser TGS-GapCloser Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser
tool_recommendation_model 0.0.5 python To update Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model
trim_galore 0.6.7 0.6.10 trim-galore To update trim_galore Trim Galore Sequence trimming Sequence analysis Trim Galore adaptive quality and adapter trimmer A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore
uniprot_rest_interface 0.4 requests To update UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface
vt 0.2 2015.11.10 vt To update A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt bgruening https://github.com/atks/vt
wtdbg 2.5 2.5 wtdbg Up-to-date wtdbg2 wtdbg2 Genome assembly, De-novo assembly Sequence assembly, Sequencing WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg
align_back_trans 0.0.10 1.70 biopython To update Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
chromosome_diagram 0.0.3 1.70 biopython To update Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram peterjc
clc_assembly_cell 0.0.7 1.19.2 samtools To update Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell
clinod 0.1.0 1.3 clinod To update NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
count_roi_variants 0.0.6 1.19.2 samtools To update Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants
coverage_stats 0.1.0 1.19.2 samtools To update BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats
effectiveT3 0.0.20 1.0.1 effectiveT3 To update Find bacterial type III effectors in protein sequences To update http://effectors.org Sequence Analysis effectivet3 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
fasta_filter_by_id 0.0.7 1.1.5 galaxy_sequence_utils To update Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id
fastq_filter_by_id 0.0.7 1.1.5 galaxy_sequence_utils To update Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id
fastq_pair_names 0.0.5 1.1.5 galaxy_sequence_utils To update Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names
fastq_paired_unpaired 0.1.5 1.1.5 galaxy_sequence_utils To update Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired
get_orfs_or_cdss 0.2.3 1.70 biopython To update Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss
mummer 0.0.8 9.18 ghostscript To update Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer
nlstradamus 0.0.11 1.8 NLStradamus To update Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus
predictnls 0.0.10 To update Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls
protein_analysis 0.0.13 promoter To update TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis
sample_seqs 0.2.6 1.70 biopython To update Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs
samtools_depad 0.0.5 1.19.2 samtools To update Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad
samtools_depth 0.0.3 1.19.2 samtools To update Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth
samtools_idxstats 0.0.6 1.19.2 samtools To update BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
seq_composition 0.0.5 1.70 biopython To update Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition
seq_filter_by_id 0.2.9 1.70 biopython To update Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id
seq_filter_by_mapping 0.0.8 1.70 biopython To update Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping
seq_length 0.0.5 1.70 biopython To update Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length
seq_primer_clip 0.0.18 1.1.5 galaxy_sequence_utils To update Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip
seq_rename 0.0.10 1.1.5 galaxy_sequence_utils To update Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename
seq_select_by_id 0.0.15 1.70 biopython To update Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id
venn_list 0.1.2 1.1.5 galaxy_sequence_utils To update Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list
TrimNs 0.1.0 1.0 trimns_vgp To update TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN
abricate 1.0.1 1.0.1 abricate Up-to-date ABRicate ABRicate Antimicrobial resistance prediction Genomics, Microbiology Mass screening of contigs for antiobiotic resistance genes Mass screening of contigs for antimicrobial resistance or virulence genes. Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/
abritamr 1.0.14 1.0.14 abritamr Up-to-date A pipeline for running AMRfinderPlus and collating results into functional classes Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr
abyss 2.3.7 2.3.7 abyss Up-to-date abyss ABySS Genome assembly, De-novo assembly, Scaffolding Sequence assembly Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler De novo genome sequence assembler using short reads. Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss
adapter_removal 2.3.3 2.3.3 adapterremoval Up-to-date adapterremoval AdapterRemoval Sequence trimming, Sequence merging, Primer removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/
add_input_name_as_column 0.2.0 python To update Add input name as column on an existing tabular file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation add_input_name_as_column mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column
aegean 0.16.0 0.16.0 aegean Up-to-date gaeval GAEVAL Sequence annotation Sequence analysis, Gene structure AEGeAn toolkit wrappers Gene Annotation EVAluation. Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean
aldex2 1.26.0 1.34.0 bioconductor-aldex2 To update aldex2 ALDEx2 Statistical inference Gene expression, Statistics and probability Performs analysis Of differential abundance taking sample variation into account A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2
allegro @VER@.0 3 allegro To update allegro Allegro Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA Linkage and haplotype analysis from deCODE It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. To update http://www.decode.com/software/ Variant Analysis allegro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/
amplican 1.14.0 1.24.0 bioconductor-amplican To update amplican amplican Alignment, Standardisation and normalisation PCR experiment, Statistics and probability AmpliCan is an analysis tool for genome editing. It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. To update https://github.com/valenlab/amplican Sequence Analysis amplican iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican
ampvis2 2.8.6 To update ampvis ampvis Analysis, Visualisation Biodiversity ampvis2 ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2
amrfinderplus 3.11.26 3.12.8 ncbi-amrfinderplus To update amrfinderplus AMRFinderPlus Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms To update https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus
ancombc 1.4.0 2.4.0 bioconductor-ancombc To update ancombc ANCOMBC DNA barcoding Microbial ecology, Metagenomics Performs analysis of compositions of microbiomes with bias correction. Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc
anndata 0.10.3 0.6.22.post1 anndata To update Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis anndata iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/
annotatemyids 3.18.0 3.18.0 bioconductor-org.hs.eg.db Up-to-date annotatemyids annotatemyids Annotation annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids
arriba 2.4.0 2.4.0 arriba Up-to-date Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba
art 2014.11.03.0 2016.06.05 art To update art ART Conversion Bioinformatics Simulator for Illumina, 454, and SOLiD sequencing data ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD To update Sequence Analysis, Data Source art iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art
artic 1.2.4 artic To update artic ARTIC Sequence alignment Genomics The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic
assembly-stats 17.02 17.02 rjchallis-assembly-stats Up-to-date Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats
augustus 3.4.0 3.5.0 augustus To update augustus AUGUSTUS Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus
b2btools 3.0.5+galaxy0 3.0.6 b2btools To update b2btools b2bTools Protein disorder prediction, Protein secondary structure prediction, Protein feature detection This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology iuc
bakta 1.9.2 1.9.2 bakta Up-to-date Bakta Bakta Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis "Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta
bam_to_scidx 1.0.1 openjdk To update Contains a tool that converts a BAM file to an ScIdx file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats bam_to_scidx iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx
bamutil 1.0.15 bamutil To update bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil
bandage 2022.09 2022.09 bandage_ng Up-to-date bandage Bandage Sequence assembly visualisation Genomics, Sequence assembly Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Up-to-date https://github.com/rrwick/Bandage Visualization bandage iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage
barcode_splitter 0.18.6 barcode_splitter To update A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter
baredsc 1.1.2 1.1.2 baredsc Up-to-date baredsc baredSC Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization baredsc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc
barrnap 1.2.2 0.9 barrnap To update barrnap Barrnap Gene prediction Genomics, Model organisms, Model organisms Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). To update Sequence Analysis barrnap iuc
basil 1.2.0 1.2.0 anise_basil Up-to-date Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil iuc
bax2bam 0.0.11 0.0.11 bax2bam Up-to-date BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam
bayescan 2.1 2.0.1 bayescan To update bayescan BayeScan Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism Detecting natural selection from population-based genetic data BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/
bbtools 39.06 39.06 bbmap Up-to-date BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools
bcftools 1.15.1 1.19 bcftools To update bcftools BCFtools Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment BCFtools toolkit wrappers BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. To update https://samtools.github.io/bcftools/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools
bctools 0.2.2 0.2.2 bctools Up-to-date bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
beacon2 2.0.0 2.0.0 beacon2-ri-tools Up-to-date GA4GH Beacon beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis beacon2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2
beagle 5.2_21Apr21.304 5.4_22Jul22.46e beagle To update Beagle is a program for phasing and imputing missing genotypes. To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis beagle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle
bedops 2.4.41 2.4.41 bedops Up-to-date BEDOPS: high-performance genomic feature operations Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations bedops_sortbed iuc https://bedops.readthedocs.io/
bedtools 2.30.0 2.31.1 bedtools To update bedtools BEDTools Mapping Genomics bedtools is a powerful toolset for genome arithmetic BEDTools is an extensive suite of utilities for comparing genomic features in BED format. To update https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation bedtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
bellerophon 1.0 1.0 bellerophon Up-to-date Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon iuc https://github.com/davebx/bellerophon
berokka 0.2.3 0.2.3 berokka Up-to-date Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka
bigscape 1.1.9 1.1.9 bigscape Up-to-date Construct sequence similarity networks of BGCs and groups them into GCF Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/
binning_refiner 1.4.3 1.4.3 binning_refiner Up-to-date binning_refiner Binning_refiner Read binning, Sequence clustering Metagenomics Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. Improving genome bins through the combination of different binning programs Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/
bioext 0.21.2 0.21.2 python-bioext Up-to-date A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! Up-to-date https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers iuc https://github.com/davebx/bioext-gx/
bioinformatics_cafe 0.1.0 python To update Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe
biom_format 2.1.15 2.1.7 biom-format To update biomformat biomformat Formatting Laboratory information management, Sequence analysis The biom-format package provides a command line interface and Python API for working with BIOM files. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format
bioperl 1.1 1.7.8 perl-bioperl To update bioperl BioPerl Data handling, Service invocation Genomics, Software engineering, Data management Converts GenBank format files to GFF3 A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl
biscot 2.3.3 2.3.3 biscot Up-to-date Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot iuc https://github.com/bgruening/iuc/tree/master/tools/biscot
blast 1.7.0 1.7.0 magicblast Up-to-date Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast
blastxml_to_gapped_gff3 1.1 0.6.6 bcbiogff To update BlastXML to gapped GFF3 To update Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3
bowtie2 2.5.3 2.5.3 bowtie2 Up-to-date bowtie2 Bowtie 2 Read mapping Mapping, Genomics, Mapping Bowtie2: Fast and sensitive read alignment Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Up-to-date http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2
bracken 2.9 2.9 bracken Up-to-date bracken Bracken Statistical calculation Metagenomics, Microbial ecology Bayesian Reestimation of Abundance with KrakEN Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken
breseq 0.35.5 0.38.3 breseq To update breseq breseq Polymorphism detection Sequencing, Sequence analysis, DNA mutation Predicts mutations in microbial genomes Runs Breseq software on a set of fastq files. To update https://github.com/barricklab/breseq Variant Analysis breseq iuc
busco 5.5.0 5.6.1 busco To update busco BUSCO Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis BUSCO assess genome and annotation completeness Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/
bwa 0.7.17 0.7.17 bwa Up-to-date bwa BWA Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Wrapper for bwa mem, aln, sampe, and samse Fast, accurate, memory-efficient aligner for short and long sequencing reads Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa
bwa_mem2 2.2.1 2.2.1 bwa-mem2 Up-to-date bwa-mem2 Bwa-mem2 Sequence alignment Mapping Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2
bwameth 0.2.6 0.2.7 bwameth To update Fast and accurate alignment of BS-seq reads To update https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth
cactus 2.7.1 To update cactus Cactus Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics Cactus is a reference-free whole-genome multiple alignment program Cactus is a reference-free whole-genome multiple alignment program. To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus
calculate_contrast_threshold 1.0.0 numpy To update Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold
calculate_numeric_param 0.1.0 To update Calculate a numeric parameter value using integer and float values. To update Text Manipulation calculate_numeric_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param
cat 5.2.3 5.3 cat To update cat_bins CAT and BAT Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly Contig Annotation Tool (CAT) Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat
cdhit 4.8.1 4.8.1 cd-hit Up-to-date cd-hit cd-hit Sequence clustering Sequencing Cluster or compare biological sequence datasets Cluster a nucleotide dataset into representative sequences. Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit
cemitool 1.18.1 1.26.0 bioconductor-cemitool To update cemitool CEMiTool Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Gene co-expression network analysis tool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. To update https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool
charts 1.0.1 r-getopt To update Enables advanced visualization options in Galaxy Charts To update Visualization charts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/
checkm 1.2.0 1.2.2 checkm-genome To update checkm CheckM Operation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. To update https://github.com/Ecogenomics/CheckM Metagenomics checkm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm
cherri 0.7 0.8 cherri To update cherri cherri Molecular interactions, pathways and networks, Structure analysis, Machine learning Computational Help Evaluating RNA-RNA interactions CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri
chira 1.4.3 1.4.3 chira Up-to-date chira ChiRA RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Chimeric Read Annotator for RNA-RNA interactome data ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira
chopin2 1.0.7 chopin2 To update Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2
chromeister 1.5.a 1.5.a chromeister Up-to-date ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister
circexplorer2 2.3.8 2.3.8 circexplorer2 Up-to-date circexplorer2 CIRCexplorer2 RNA splicing, Gene transcripts, Literature and language Comprehensive and integrative circular RNA analysis toolset. Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2
circos 0.69.8 0.69.9 circos To update galactic_circos Galactic Circos Sequence visualisation Build Circos Plots in Galaxy Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. To update http://circos.ca/ Graphics circos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos
cite_seq_count 1.4.4 1.4.4 cite-seq-count Up-to-date CITE-seq-Count CITE-seq-Count RNA-Seq quantification Transcriptomics, Immunoproteins and antigens Count CMO/HTO Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. Up-to-date https://github.com/Hoohm/CITE-seq-Count Transcriptomics cite_seq_count iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count
clair3 0.1.12 1.0.5 clair3 To update clair3 Clair3 Variant calling Molecular genetics Symphonizing pileup and full-alignment for high-performance long-read variant calling Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3
clustalw 2.1 2.1 clustalw Up-to-date \n clustal2\n ClustalW multiple sequence alignment program for DNA or proteins Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw
cnv-phenopacket 1.0.2 cnv-phenopacket To update cnv-phenopacket Converts TSV metadata file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv_phenopacket iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket
cnv-vcf2json 1.0.4 cnv-vcf2json To update cnv-vcf2json Converts structural variants VCF file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv-vcf2json iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json
cnvkit 0.9.10 0.9.10 cnvkit Up-to-date cnvkit CNVkit Variant calling DNA structural variation detecting copy number variants and alterations genome-wide from high-throughput sequencing CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit
codeml 4.9 4.10.7 paml To update paml PAML Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis Detects positive selection Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml
cojac 0.9.1 0.9.1 cojac Up-to-date cojac COJAC Genetic variation co-occurrence of mutations on amplicons CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac
colibread 24.7.14+galaxy0 24.7.14 commet To update Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread
collection_column_join 0.0.3 8.25 coreutils To update Column Join on Collections To update Text Manipulation collection_column_join iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join
collection_element_identifiers 0.0.2 To update Extract element identifiers of a collection To update Text Manipulation collection_element_identifiers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers
column_maker 2.0 python To update Compute an expression on every row To update Text Manipulation column_maker devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker
column_order_header_sort 0.0.1 python To update Sort Column Order by heading To update Text Manipulation column_order_header_sort iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort
column_remove_by_header 1.0 python To update Remove columns by header To update Text Manipulation column_remove_by_header iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header
compleasm 0.2.5 0.2.5 compleasm Up-to-date Compleasm: a faster and more accurate reimplementation of BUSCO Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/
compose_text_param 0.1.1 To update Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param
compress_file 0.1.0 gzip To update Compress files. To update Text Manipulation compress_file iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file
concoct 1.1.0 1.1.0 concoct Up-to-date concoct CONCOCT Sequence clustering, Read binning Metagenomics CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct
coverage_report 0.0.4 1.76 perl-number-format To update Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report
coverm 0.7.0 0.7.0 coverm Up-to-date coverm CoverM Local alignment Bioinformatics CoverM genome and contig wrappers Read coverage calculator for metagenomics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm iuc https://github.com/galaxyproject/tools-iuc/tools/coverm
crispr_studio 1+galaxy0 1 crispr_studio To update CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/
crosscontamination_barcode_filter 0.3 2.2.1 r-ggplot2 To update Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter
crossmap 0.6.1 0.7.0 crossmap To update CrossMap converts genome coordinates or annotation files between genome assemblies To update http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap
cutadapt 4.6 4.6 cutadapt Up-to-date cutadapt Cutadapt Sequence trimming Genomics, Probes and primers, Sequencing Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt
cutesv 1.0.8 2.1.0 cutesv To update cuteSV cuteSV Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis To update https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv
cwpair2 1.1.1 matplotlib To update Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2
dada2 1.30.0 bioconductor-dada2 To update dada2 dada2 Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics DADA2 wrappers 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. To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2
das_tool 1.1.7 1.1.7 das_tool Up-to-date dastool dastool Read binning Metagenomics DAS Tool for genome resolved metagenomics DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool
data_source_iris_tcga 1.0.0 python To update IRIS-TCGA Data source tool To update Data Source data_source_iris_tcga iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga
datamash 1.8 1.1.0 datamash To update GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. To update https://www.gnu.org/software/datamash/ Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash
decontaminator 1.0.0 numpy To update decontaminator Deep Learning method for novel virus detection in sequencing data To update https://github.com/cbib/decontaminator Machine Learning decontaminator iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator
deepmicro 1.4 1.4 deepmicro Up-to-date \n DeepMicro\n Representation learning and classification framework Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro iuc https://github.com/paulzierep/DeepMicro
deepsig 1.2.5 1.2.5 deepsig Up-to-date Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig
deepvariant 1.5.0 To update DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant
deg_annotate 1.1.0 2.31.1 bedtools To update Annotate DESeq2/DEXSeq output tables To update Transcriptomics deg_annotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate
delly 0.9.1 1.2.6 delly To update delly2 Delly2 Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. To update https://github.com/dellytools/delly Variant Analysis delly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly
deseq2 1.42.0 bioconductor-deseq2 To update DESeq2 DESeq2 Differential gene expression analysis Transcriptomics Differential gene expression analysis based on the negative binomial distribution R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2
dexseq 1.44 1.48.0 bioconductor-dexseq To update dexseq DEXSeq Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Inference of differential exon usage in RNA-Seq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. To update https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq
diamond 2.0.15 2.1.9 diamond To update diamond Diamond Sequence alignment analysis Sequence analysis, Proteins DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond
diffbind 2.10.0 3.12.0 bioconductor-diffbind To update diffbind DiffBind Differential binding analysis ChIP-seq Diffbind provides functions for processing ChIP-Seq data. Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind
dimet 0.2.1 0.2.2 dimet To update DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. To update https://github.com/cbib/DIMet Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet
disco 1.2 disco To update disco DISCO Protein sequence analysis Structure determination DISCO is a overlap-layout-consensus (OLC) metagenome assembler DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. To update http://disco.omicsbio.org/ Metagenomics, Assembly disco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/
dnabot 3.1.0 dnabot To update DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot
dnaweaver 1.0.2 1.0.2 dnaweaver_synbiocad Up-to-date Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver
dram 1.3.5 1.4.6 dram To update dram DRAM Gene functional annotation Metagenomics, Biological databases, Molecular genetics DRAM for distilling microbial metabolism to automate the curation of microbiome function Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram
drep 3.4.5 3.5.0 drep To update drep dRep Genome comparison Metagenomics, Genomics, Sequence analysis dRep compares and dereplicates genome sets Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. To update https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep
dropletutils 1.10.0 1.22.0 bioconductor-dropletutils To update dropletutils DropletUtils Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Transcriptomics, Sequence Analysis dropletutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/
ebi_tools 0.1.0 six To update Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools
edger 3.36.0 4.0.2 bioconductor-edger To update edger edgeR Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq Perform RNA-Seq differential expression analysis using edgeR pipeline Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger
egsea 1.20.0 1.28.0 bioconductor-egsea To update egsea EGSEA Gene set testing Systems biology This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea
emboss_5 5.0.0 6.6.0 emboss To update emboss EMBOSS Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology Galaxy wrappers for EMBOSS version 5.0.0 tools Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5
ena_upload 0.6.3 0.7.1 ena-upload-cli To update Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). To update https://github.com/usegalaxy-eu/ena-upload-cli Data Export ena_upload iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload
enasearch 0.2.2 enasearch To update A Python library for interacting with ENA's API To update https://github.com/bebatut/enasearch Data Source enasearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch
ensembl_vep 110.1 111.0 ensembl-vep To update Ensembl VEP: Annotate VCFs with variant effect predictions To update https://github.com/Ensembl/ensembl-vep Variant Analysis ensembl_vep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep
episcanpy 0.3.2 0.4.0 episcanpy To update episcanpy epiScanpy Enrichment analysis, Imputation Epigenomics, Cell biology, DNA EpiScanpy – Epigenomics single cell analysis in python Epigenomics Single Cell Analysis in Python. To update https://github.com/colomemaria/epiScanpy Epigenetics episcanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/
exomedepth 1.1.0 1.1.16 r-exomedepth To update exomedepth ExomeDepth Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth
exonerate 2.4.0 2.4.0 exonerate Up-to-date exonerate Exonerate Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Exonerate is a generic tool for pairwise sequence comparison. A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate
export2graphlan 0.20 0.22 export2graphlan To update export2graphlan export2graphlan Conversion Taxonomy, Metabolomics, Biomarkers export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn 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. To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/
extract_genomic_dna 3.0.3+galaxy2 0.11.0 bx-python To update Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna
fargene 0.1 0.1 fargene Up-to-date fargene fARGene Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene
fasta_nucleotide_color_plot 1.0.1 openjdk To update Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot
fasta_stats 2.0 numpy To update Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/
fastani 1.3 1.34 fastani To update Fast alignment-free computation of whole-genome Average Nucleotide Identity To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani iuc
fastp 0.23.4 fastp To update \n fastp\n Fast all-in-one preprocessing for FASTQ files To update https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp
fastqc 0.74+galaxy0 0.12.1 fastqc To update fastqc FastQC Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis Read QC reports using FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc
fastqe 0.3.1+galaxy0 0.3.1 fastqe To update fastqe FASTQE Sequencing quality control Sequence analysis, Sequencing FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. To update https://fastqe.com/ Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe
fasttree 2.1.10 2.1.11 fasttree To update fasttree FastTree Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree
featurecounts 2.0.3 2.0.6 subread To update featurecounts FeatureCounts Read summarisation Sequencing featureCounts counts the number of reads aligned to defined masked regions in a reference genome featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts
feelnc 0.2.1 0.2 feelnc To update feelnc FEELnc Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA Galaxy wrapper for FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc
fermikit r193 r193 fermi2 Up-to-date FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit
fgsea 1.8.0+galaxy1 1.28.0 bioconductor-fgsea To update fgsea fgsea Gene-set enrichment analysis Genetics Perform gene set testing using fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea
filtlong 0.2.1 0.2.1 filtlong Up-to-date \n filtlong\n Filtlong - Filtering long reads by quality Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong
flair 1.5 2.0.0 flair To update FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair
flash 1.2.11 1.2.11 flash Up-to-date flash FLASH Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Fast Length Adjustment of SHort reads Identifies paired-end reads which overlap in the middle, converting them to single long reads Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash
fraggenescan 1.31 fraggenescan To update fraggenescan FragGeneScan Gene prediction Genetics, Sequence analysis Tool for finding (fragmented) genes in short read Application for finding (fragmented) genes in short reads To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/
freebayes 1.3.6 1.3.7 freebayes To update freebayes FreeBayes Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases Galaxy Freebayes Bayesian genetic variant detector tool Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. To update https://github.com/ekg/freebayes Variant Analysis freebayes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes
freec 11.6 gawk To update freec FREEC Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis control_freec iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec
freyja 1.4.4 1.4.9 freyja To update freyja lineage abundances estimation To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja
fsd 1.0.2 matplotlib To update Tool that plots a histogram of sizes of read families To update Graphics duplex_family_size_distribution iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd
funannotate 1.8.15 To update \n funannotate\n Funannotate is a genome prediction, annotation, and comparison software package. To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate
gatk4 gatk4 To update A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4
gdcwebapp 1.0.0 python To update GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy
gecko 1.2 1.2 gecko Up-to-date Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko
gemini 0.20.1 0.30.2 gemini To update gemini GEMINI Sequence analysis, Genetic variation analysis Sequence analysis GEMINI: a flexible framework for exploring genome variation GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini
genebed_maf_to_fasta 1.0.1+galaxy0 To update Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/
genehunter_modscore 3.0.0 3.1 ghm To update Maximised LOD score pedigree analysis utility To update https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html Variant Analysis genehunter_modscore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/
geneiobio 4.7.1+galaxy1 To update Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio
genetrack numpy To update Contains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand. To update ChIP-seq genetrack iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack
genomescope 2.0 2.0 genomescope2 Up-to-date Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope
genomic_super_signature 1.2.0 1.10.0 bioconductor-genomicsupersignature To update genomicsupersignature GenomicSuperSignature Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment Interpretation of RNAseq experiments through robust, efficient comparison to public databases GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature
genrich 0.5+galaxy2 0.6.1 genrich To update Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). To update https://github.com/jsh58/Genrich ChIP-seq genrich iuc https://github.com/jsh58/Genrich
get_hrun pyfaidx To update Annotate indel variants with homopolymer context To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis get_hrun iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun
getorganelle getorganelle Up-to-date getorganelle GetOrganelle De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle
gfa_to_fa 0.1.2 To update gfa_to_fa - Converting GFA format to Fasta format To update http://gfa-spec.github.io/GFA-spec/ Convert Formats gfa_to_fa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa
gff3_rebase 1.2 0.6.6 bcbiogff To update Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase
gffcompare 0.12.6 0.12.6 gffcompare Up-to-date gffcompare gffcompare Sequence annotation Nucleic acids, Sequence analysis Galaxy wrappers for Geo Pertea's GffCompare package. Program for comparing, annotating, merging and tracking transcripts in GFF files. Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare
gffread 0.12.7 0.12.7 gffread Up-to-date gffread gffread Sequence annotation Nucleic acids, Sequence analysis gffread filters and/or converts GFF3/GTF2 records program for filtering, converting and manipulating GFF files Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread
ggplot2 3.4.0 r-base To update ggplot2 ggplot2 Visualisation Data visualisation ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. Plotting system for R, based on the grammar of graphics. To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2
ggupset 1.0 r-ggupset To update Create Upset Plots with ggupset To update https://github.com/const-ae/ggupset Graphics ggupset iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset
glimmer 3.02 glimmer To update gemini GEMINI Sequence analysis, Genetic variation analysis Sequence analysis Glimmer makes gene predictions. GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer
goenrichment 2.0.1 2.0.1 goenrichment Up-to-date goenrichment GOEnrichment Gene-set enrichment analysis Transcriptomics Performs GO Enrichment analysis. GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment
goseq 1.50.0 1.54.0 bioconductor-goseq To update goseq GOseq Gene functional annotation RNA-Seq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq
gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 To update functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/
graphembed 2.4 2.4 graph_embed Up-to-date Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/
graphlan 1.1.3 graphlan To update graphlan GraPhlAn Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees 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. To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/
gtdbtk 2.3.2 2.3.2 gtdbtk Up-to-date GTDB-Tk GTDB-Tk Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Up-to-date https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk
gtfToBed12 357 447 ucsc-gtftogenepred To update UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Sequence analysis Convert GTF files to BED12 format Utilities for handling sequences and assemblies from the UCSC Genome Browser project. To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats gtftobed12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12
gubbins 3.2.1 3.3.3 gubbins To update gubbins Gubbins Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing Gubbins - bacterial recombination detection Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins
gvcftools 0.1 0.17.0 gvcftools To update To update https://github.com/sequencing/gvcftools Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools
gwastools 0.1.0 1.48.0 bioconductor-gwastools To update gwastools GWASTools Deposition, Analysis, Annotation GWAS study Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis iuc
hamronization 1.0.3 1.1.4 hamronization To update hamronization hAMRonization Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Convert AMR gene detection tool output to hAMRonization specification format. Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure To update https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization
hansel 2.6.1 2.6.1 bio_hansel Up-to-date Biohansel BioHansel Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Heidelberg and Enteritidis SNP Elucidation BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel
hapcut2 1.3.3 1.3.3 hapcut2 Up-to-date hapcut2 HapCUT2 Haplotype mapping, Variant classification Robust and accurate haplotype assembly for diverse sequencing technologies 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 Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 galaxy-australia https://github.com/galaxyproject/tools-iuc
hapog 1.3.7 1.3.7 hapog Up-to-date hapog Hapo-G Genome assembly, Optimisation and refinement Sequence assembly, Genomics Hapo-G - Haplotype-Aware Polishing of Genomes 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. Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog
happy 0.3.14 0.3.15 hap.py To update hap.py hap.py Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. To update https://github.com/Illumina/hap.py Variant Analysis happy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy
heatmap2 2.17.0 r-gplots To update heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2
heinz 1.0 1.62.0 bioconductor-bionet To update bionet BioNet Protein interaction analysis Molecular interactions, pathways and networks, Protein interactions An algorithm for identification of the optimal scoring subnetwork. This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork. To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz
hicexplorer 3.7.2 3.7.3 hicexplorer To update HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. To update https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer
hicstuff 3.1.5 3.2.2 hicstuff To update To update https://github.com/koszullab/hicstuff Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff
hifiasm_meta 0.3.1 hamtv0.3.1 hifiasm_meta To update hifiasm-meta Hifiasm-meta Sequence assembly Sequence assembly, Metagenomics A hifiasm fork for metagenome assembly using Hifi reads. Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta
hisat2 2.2.1 2.2.1 hisat2 Up-to-date hisat2 HISAT2 Sequence alignment RNA-seq HISAT2 is a fast and sensitive spliced alignment program. 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). Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2
hivclustering 1.3.1 1.6.8 python-hivclustering To update Infers transmission networks from pairwise distances inferred by tn93 To update https://pypi.org/project/hivclustering/ Next Gen Mappers hivclustering iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/
hmmer3 3.4 3.4 hmmer Up-to-date hmmer3 HMMER3 Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Up-to-date http://hmmer.org/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3
homer 4.11 4.11 homer Up-to-date homer homer Sequence motif discovery HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer
htseq_count 2.0.5 2.0.5 htseq Up-to-date htseq HTSeq Nucleic acid sequence analysis Sequence analysis Count aligned reads (SAM/BAM) that overlap genomic features (GFF) Python framework to process and analyse high-throughput sequencing (HTS) data Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count
humann 3.8 3.8 humann Up-to-date humann humann Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann
hybpiper 2.1.6 2.1.6 hybpiper Up-to-date HybPiper HybPiper Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Analyse targeted sequence capture data Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Up-to-date https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper
hyphy 2.5.47 2.5.59 hyphy To update HyPhy HyPhy Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks Hypothesis Testing using Phylogenies Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. To update http://www.hyphy.org Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/
hypo 1.0.3 1.0.3 hypo Up-to-date HyPo HyPo Optimisation and refinement, Genome assembly Sequence assembly, Genomics Super Fast & Accurate Polisher for Long Read Genome Assemblies 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. Up-to-date https://github.com/kensung-lab/hypo Assembly hypo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo
icescreen 1.3.1 1.3.2 icescreen To update icescreen ICEscreen Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen
idba_ud 1.1.3 idba To update idba IDBA Sequence assembly Sequence assembly Wrappers for the idba assembler variants. A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud
idr 2.0.3 idr To update Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/
idr_download 0.44.1 5.11.1 omero-py To update Image Data Resource downloading tool To update https://idr.openmicroscopy.org Data Source idr_download_by_ids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download
iedb_api 2.15.2 python To update Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api
instrain 1.5.3 1.8.0 instrain To update instrain InStrain SNP detection, Genome comparison Mapping, Metagenomics InStrain is a tool for analysis of co-occurring genome populations from metagenomes InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain
integron_finder 2.0.3 2.0.3 integron_finder Up-to-date integron_finder Integron Finder Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis "IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching" A tool to detect Integron in DNA sequences. Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder
intermine_galaxy_exchange 0.0.1 8.25 coreutils To update InterMine Exporter To update Convert Formats intermine_galaxy_exchange iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange
interproscan 5.59-91.0 interproscan To update interproscan_ebi InterProScan (EBI) Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis Interproscan queries the interpro database and provides annotations. Scan sequences against the InterPro protein signature databases. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan
interval2maf 1.0.1+galaxy1 0.11.0 bx-python To update bx-python bx-python Sequence analysis Extract MAF blocks given a set of intervals Tools for manipulating biological data, particularly multiple sequence alignments. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations interval2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/
intervene 0.6.5 0.6.5 intervene Up-to-date intervene Intervene Sequence comparison, Sequence visualisation Computational biology Create pairwise and upset plots Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Up-to-date https://intervene.readthedocs.io Statistics intervene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene
iqtree 2.1.2 2.2.6 iqtree To update Efficient phylogenomic software by maximum likelihood To update http://www.iqtree.org/ Phylogenetics iqtree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/
irissv 1.0.4 1.19.2 samtools To update Refine insertion sequences To update https://github.com/mkirsche/Iris Variant Analysis irissv iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/
isescan isescan To update ISEScan ISEScan Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation "ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements." Automated identification of insertion sequence elements in prokaryotic genomes. To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan
isoformswitchanalyzer 1.20.0 2.2.0 bioconductor-isoformswitchanalyzer To update IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Sequence comparison, Sequence analysis Computational biology, Gene transcripts Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer
ivar 1.4.2 1.4.2 ivar Up-to-date iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/
iwtomics 1.0.0 1.26.0 bioconductor-iwtomics To update iwtomics IWTomics Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability Interval-Wise Testing for Omics Data Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset. To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics
jasminesv 1.0.11 1.1.5 jasminesv To update Merge structural variants across samples To update https://github.com/mkirsche/Jasmine/ Variant Analysis jasminesv iuc https://github.com/galaxyproject/tools-iuc/jasminesv/
jbrowse 1.16.11 1.16.11 jbrowse Up-to-date jbrowse JBrowse Genome visualisation Genomics JBrowse Genome Browser integrated as a Galaxy Tool Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Up-to-date https://jbrowse.org Sequence Analysis jbrowse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse
jcvi_gff_stats 0.8.4 1.3.9 jcvi To update Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats
jellyfish 2.3.1 kmer-jellyfish To update Jellyfish Jellyfish k-mer counting Sequence analysis, Genomics Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA A command-line algorithm for counting k-mers in DNA sequence. To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish
join_files_by_id 1.0 1.11.6 r-data.table To update This tool will join datasets according to a column with identifier To update Text Manipulation join_files_by_id iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id
jq 1.0 1.5 jq To update JQ is a lightweight and flexible command-line JSON processor To update https://stedolan.github.io/jq/ Text Manipulation jq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq
jvarkit 20201223 20201223 jvarkit-wgscoverageplotter Up-to-date Jvarkit : Java utilities for Bioinformatics Up-to-date https://lindenb.github.io/jvarkit/ SAM jvarkit iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit
kallisto 0.48.0 0.50.1 kallisto To update kallisto kallisto Gene expression profiling Transcriptomics, RNA-seq, Gene expression kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. To update https://pachterlab.github.io/kallisto/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/
kc-align 1.0.2 1.0.2 kcalign Up-to-date kc-align kc-align Multiple sequence alignment Mapping Kc-Align custom tool A fast and accurate tool for performing codon-aware multiple sequence alignments Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align
khmer 3.0.0a3 3.0.0a3 khmer Up-to-date khmer khmer Standardisation and normalisation, De-novo assembly Sequence assembly In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer
king 2.2.7 2.2.7 king Up-to-date Kinship-based INference for Gwas Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis king iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/
kleborate 2.3.2 2.3.2 kleborate Up-to-date kleborate Kleborate Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate
kma 1.2.21 1.4.14 kma To update Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma
kofamscan 1.3.0 1.3.0 kofamscan Up-to-date Gene function annotation tool based on KEGG Orthology and hidden Markov model Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan
kraken_biom 1.2.0 1.2.0 kraken-biom Up-to-date Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom
kraken_taxonomy_report 0.0.3 1.70 biopython To update Kraken taxonomy report To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report
krakentools 1.2 1.2 krakentools Up-to-date krakentools KrakenTools Visualisation, Aggregation Taxonomy, Metagenomics KrakenTools is a suite of scripts to be used alongside the Kraken KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools
krocus 1.0.1 1.0.3 krocus To update Predict MLST directly from uncorrected long reads To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus
last 1205 1542 last To update last LAST Sequence alignment Genomics, Comparative genomics LAST finds similar regions between sequences. Short read alignment program incorporating quality scores To update http://last.cbrc.jp/ Sequence Analysis last iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last
lastz 1.04.22 1.04.22 lastz Up-to-date lastz LASTZ Sequence alignment, Read mapping Genomics Galaxy wrappers for the Lastz and Lastz_d A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. Up-to-date https://github.com/lastz/lastz Next Gen Mappers lastz devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz
lcrgenie 1.0.2 lcr_genie To update Ligase Chain Reaction Genie To update https://github.com/neilswainston/LCRGenie Synthetic Biology lcrgenie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie
legsta 0.5.1 0.5.1 legsta Up-to-date Performs in silico Legionella pneumophila sequence based typing. Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta iuc https://github.com/tseemann/legsta
length_and_gc_content 0.1.2 1.3.2 r-optparse To update Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content
limma_voom 3.58.1 3.58.1 bioconductor-limma Up-to-date limma limma RNA-Seq analysis Molecular biology, Genetics Perform RNA-Seq differential expression analysis using limma voom pipeline Data analysis, linear models and differential expression for microarray data. Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom
lineagespot 1.6.0 r-base To update lineagespot lineagespot Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot
links 2.0.1 2.0.1 links Up-to-date links LINKS Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Scaffold genome assemblies with long reads. 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. Up-to-date https://github.com/bcgsc/LINKS Assembly links iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links
lofreq 2.1.5 2.1.5 lofreq Up-to-date LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. Up-to-date https://csb5.github.io/lofreq/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq
lorikeet 20 20 lorikeet Up-to-date Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet
lumpy_sv 0.3.1 0.3.1 lumpy-sv Up-to-date LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv iuc https://github.com/arq5x/lumpy-sv
m6anet 2.1.0 2.1.0 m6anet Up-to-date m6Anet m6Anet Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning m6anet to detect m6A RNA modifications from nanopore data Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet
maaslin2 0.99.12 0.99.12 maaslin2 Up-to-date MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 iuc https://github.com/biobakery/Maaslin2
macs2 macs2 Up-to-date macs MACS Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites MACS - Model-based Analysis of ChIP-Seq Model-based Analysis of ChIP-seq data. Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2
maf_stats 1.0.2+galaxy0 To update MAF Coverage statistics To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations maf_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/
mageck mageck To update mageck MAGeCK Genetic variation analysis Genetics, Genetic variation, Genomics Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. To update https://sourceforge.net/projects/mageck/ Genome editing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck
maker 2.31.11 3.01.03 maker To update maker MAKER Genome annotation Genomics, DNA, Sequence analysis MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker
malt 0.5.3 0.62 malt To update Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. To update https://github.com/husonlab/malt Next Gen Mappers malt_run iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt
map_param_value 0.2.0 To update Map a parameter value to another value To update Text Manipulation map_param_value iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value
mapseq 2.1.1 perl To update fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq
mash 2.3 2.3 mash Up-to-date mash Mash Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Fast genome and metagenome distance estimation using MinHash Fast genome and metagenome distance estimation using MinHash. Up-to-date https://github.com/marbl/Mash Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash
mashmap 3.1.3 3.1.3 mashmap Up-to-date Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap
masigpro 1.49.3 8.25 coreutils To update masigpro maSigPro Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq Identify significantly differential expression profiles in time-course microarray experiments Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro
maxbin2 2.2.7 maxbin2 To update maxbin MaxBin Sequence assembly Metagenomics, Sequence assembly, Microbiology clusters metagenomic contigs into bins Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/
mcl 22.282 22.282 mcl Up-to-date mcl MCL Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks The Markov Cluster Algorithm, a cluster algorithm for graphs MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl
medaka 1.7.2 1.11.3 medaka To update medaka Medaka Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning Sequence correction provided by ONT Research medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka
megahit 1.2.9 1.2.9 megahit Up-to-date megahit MEGAHIT Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit
megahit_contig2fastg 1.1.3 1.2.9 megahit To update megahit MEGAHIT Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg
megan 6.21.7 6.25.9 megan To update megan MEGAN Sequence analysis, Taxonomic classification Sequence analysis MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan
meme 5.4.1 5.5.5 meme To update meme_fimo meme_fimo Sequence motif discovery, Nucleic acid feature detection, Protein feature detection, Statistical calculation Sequence analysis, Genetic variation, Statistics and probability, Data mining The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. To update http://meme-suite.org/ ChIP-seq meme iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme
meme_chip 4.11.2 1.3.26 graphicsmagick To update Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip
meningotype 0.8.5 0.8.5 meningotype Up-to-date Assign sequence type to N. meningitidis genome assemblies Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype
merlin 1.1.2 1.1.2 merlin Up-to-date merlin Merlin Haplotype mapping, Genetic mapping GWAS study, Mapping Pedigree Analysis package Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/
merqury 1.3 1.3 merqury Up-to-date merqury Merqury Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Merqury is a tool for evaluating genomes assemblies based of k-mer operations. 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. Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury
meryl 1.3 1.3 merqury Up-to-date meryl Meryl k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Meryl a k-mer counter. Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl
metabat2 2.15 2.15 metabat2 Up-to-date MetaBAT_2 MetaBAT 2 Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/
metaeuk 5.34c21f2 6.a5d39d9 metaeuk To update MetaEuk MetaEuk Homology-based gene prediction Metagenomics, Gene and protein families MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk
metagenomeseq 1.16.0-0.0.1 1.43.0 bioconductor-metagenomeseq To update metagenomeseq metagenomeSeq Sequence visualisation, Statistical calculation Metagenomics, Sequencing metagenomeSeq Normalization 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. To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq
metaphlan 4.0.6 4.1.0 metaphlan To update metaphlan MetaPhlAn Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics MetaPhlAn for Metagenomic Phylogenetic Analysis Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. To update https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/
migmap 1.0.3 1.0.3 migmap Up-to-date MiGMAP MiGMAP Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis mapper for full-length T- and B-cell repertoire sequencing Mapper for full-length T- and B-cell repertoire sequencing. Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap
minia 3.2.6 3.2.6 minia Up-to-date minia Minia Genome assembly Sequence assembly Short-read assembler based on a de Bruijn graph Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia
miniasm 0.3_r179 0.3 miniasm To update Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm
minimap2 2.26 2.26 minimap2 Up-to-date minimap2 Minimap2 Pairwise sequence alignment Mapping A fast pairwise aligner for genomic and spliced nucleotide sequences Pairwise aligner for genomic and spliced nucleotide sequences Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2
miniprot 0.12 0.12 miniprot Up-to-date Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot
mirnature 1.1 1.1 mirnature Up-to-date Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature iuc https://github.com/Bierinformatik/miRNAture
mitobim 1.9.1 1.9.1 mitobim Up-to-date assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim
mitos 1.1.5 2.1.7 mitos To update mitos MITOS Genome annotation Zoology, Whole genome sequencing de-novo annotation of metazoan mitochondrial genomes De novo metazoan mitochondrial genome annotation. To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos
mlst 2.22.0 2.23.0 mlst To update mlst MLST Taxonomic classification Immunoproteins, genes and antigens Scan contig files against PubMLST typing schemes Multi Locus Sequence Typing from an assembled genome or from a set of reads. To update https://github.com/tseemann/mlst Sequence Analysis mlst iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst
moabs moabs To update MOABS for differential methylation analysis on Bisulfite sequencing data. To update https://github.com/sunnyisgalaxy/moabs Epigenetics moabs iuc https://github.com/sunnyisgalaxy/moabs
mosdepth 0.3.6 0.3.6 mosdepth Up-to-date fast and flexible BAM/CRAM depth calculation Up-to-date https://github.com/brentp/mosdepth SAM mosdepth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth
mothur 1.0 1.48.0 mothur To update mothur mothur DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny Mothur wrappers Open-source, platform-independent, community-supported software for describing and comparing microbial communities To update https://www.mothur.org Metagenomics mothur iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur
msaboot 0.1.2 0.1.2 msaboot Up-to-date A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot
multigps 0.74.0 fonts-conda-ecosystem To update Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps iuc
multigsea 1.12.0 1.12.0 bioconductor-multigsea Up-to-date multiGSEA multiGSEA Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules GSEA-based pathway enrichment analysis for multi-omics data A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea
multiqc 1.11 1.21 multiqc To update multiqc MultiQC Validation Sequencing, Bioinformatics MultiQC aggregates results from bioinformatics analyses across many samples into a single report MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc
mummer4 4.0.0rc1 4.0.0rc1 mummer4 Up-to-date mumer4 MUMmer4 Multiple sequence alignment Sequence analysis, Human genetics Mummer4 Tools System for rapidly aligning large DNA sequences to one another. Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4
mykrobe 0.10.0 0.13.0 mykrobe To update Mykrobe Mykrobe Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics Antibiotic resistance predictions Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe
mzmine 3.9.0 3.9.0 mzmine Up-to-date mzmine MZmine Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules mass-spectrometry data processing, with the main focus on LC-MS data Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/
naltorfs 0.1.2 0.1.2 naltorfs Up-to-date nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/
nanocompore 1.0.0rc3.post2 1.0.4 nanocompore To update Nanocompore Nanocompore Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore
nanoplot 1.41.0 1.42.0 nanoplot To update Plotting tool for long read sequencing data and alignments To update https://github.com/wdecoster/NanoPlot Visualization nanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/
nanopolishcomp 0.6.11 0.6.12 nanopolishcomp To update NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp
ncbi_acc_download 0.2.8 0.2.8 ncbi-acc-download Up-to-date Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download
ncbi_datasets 15.19.1 ncbi-datasets-cli To update ncbi_datasets NCBI Datasets Data handling, Sequence database search, Data retrieval Biological databases NCBI datasets downloads biological sequence data across all domains of life from NCBI. NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. To update https://github.com/ncbi/datasets Data Source ncbi_datasets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets
ncbi_entrez_direct 16.2 16.2 entrez-direct Up-to-date NCBI Entrez Direct allow fetching data from NCBI Databases Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct
ncbi_entrez_eutils 1.70 python To update NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils
ncbi_fcs_gx 0.5.0 0.5.0 ncbi-fcs-gx Up-to-date FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx
necat 0.0.1_update20200803 0.0.1_update20200803 necat Up-to-date necat NECAT De-novo assembly Sequence assembly Error correction and de-novo assembly for ONT Nanopore reads NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat
newick_utils 1.6+galaxy1 1.6 newick_utils To update newick_utilities Newick Utilities Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science Perform operations on Newick trees 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. To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils
nextclade 2.7.0 2.14.0 nextalign To update Identify differences between your sequences and a reference sequence used by Nextstrain To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade
ngmlr 0.2.7 0.2.7 ngmlr Up-to-date ngmlr NGMLR DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation CoNvex Gap-cost alignMents for Long Reads An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr
ngsutils 0.5.9 ngsutils To update ngsutils NGSUtils Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. NGSUtils is a suite of software tools for working with next-generation sequencing datasets To update https://github.com/ngsutils/ngsutils SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils
nonpareil 3.1.1 3.4.1 nonpareil To update Estimate average coverage in metagenomic datasets To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil
novoplasty 4.3.1 4.3.5 novoplasty To update NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty
nugen_nudup 2.3.3 2.3.3 nudup Up-to-date Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. Up-to-date http://nugentechnologies.github.io/nudup/ SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup
obitools 1.2.13 1.2.13 obitools Up-to-date obitools OBITools Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing OBITools is a set of programs developed to simplify the manipulation of sequence files Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools
ococo ococo Up-to-date Variant detection of SNVs Up-to-date https://github.com/karel-brinda/ococo Variant Analysis ococo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo
odgi 0.3 0.8.4 odgi To update Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/
omark 0.3.0 To update Proteome quality assessment software To update https://github.com/DessimozLab/OMArk Sequence Analysis omark iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/
ont_fast5_api 3.1.3 4.1.3 ont-fast5-api To update ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api
onto_toolkit 1.45 1.45 perl-onto-perl Up-to-date ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit
optdoe v2.0.2 doebase To update Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe
optitype 1.3.5 1.3.5 optitype Up-to-date Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1
orfipy 0.0.4 0.0.4 orfipy Up-to-date orfipy orfipy Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Galaxy wrapper for ORFIPY A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy
orthofinder 2.5.5 2.5.5 orthofinder Up-to-date OrthoFinder OrthoFinder Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Accurate inference of orthologous gene groups made easy OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder
packaged_annotation_loader 0.1 python To update Tool to make cached genome annotation data available as a list of datasets collection To update Data Source packaged_annotation_loader iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader
pangolin 4.3 4.3 pangolin Up-to-date Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin
parse_mito_blast 1.0.2 1.0.2 parse_mito_blast Up-to-date Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast
pathview 1.34.0 1.42.0 bioconductor-pathview To update pathview pathview Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation Pathview is a tool set for pathway based data integration and visualization. Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview
pbgcpp 2.0.2 2.0.2 pbgcpp Up-to-date genomicconsensus GenomicConsensus Variant calling Mapping Compute genomic consensus and call variants using PacBio reads mapped to a reference The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis pbgcpp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp
pbmm2 1.13.1 1.13.1 pbmm2 Up-to-date pbmm2 pbmm2 Pairwise sequence alignment, Sorting Mapping A minimap2 SMRT wrapper for PacBio data. pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Up-to-date https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2
pe_histogram 1.0.1 openjdk To update Contains a tool that produces an insert size histogram for a paired-end BAM file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics pe_histogram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram
peakzilla 1.0 python To update Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. To update https://github.com/steinmann/peakzilla ChIP-seq peakzilla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla
pear 0.9.6 0.9.6 pear Up-to-date pear PEAR Sequence merging Sequence assembly PEAR evaluates all possible paired-end read overlaps Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Up-to-date pear iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear
pharokka 1.3.2 \n pharokka\n To update \n pharokka\n rapid standardised annotation tool for bacteriophage genomes and metagenomes To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka
phyloseq 1.38.0 1.46.0 bioconductor-phyloseq To update phyloseq phyloseq Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Handling and analysis of high-throughput microbiome census data Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. To update https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq
phyml 3.3.20220408 3.3.20220408 phyml Up-to-date phyml PhyML Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics PhyML is a phylogeny software based on the maximum-likelihood principle. Phylogenetic estimation software using Maximum Likelihood Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml
picard 3.1.1 3.1.1 picard Up-to-date picard_fastqtosam picard_fastqtosam Formatting Sequencing Picard SAM/BAM manipulation tools. Create an unaligned BAM file. Up-to-date http://broadinstitute.github.io/picard/ SAM picard devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard
pick_value 0.2.0 To update Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value
picrust 1.1.1 1.1.4 picrust To update picrust PICRUSt Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing PICRUSt wrappers PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust
picrust2 2.5.1 2.5.2 picrust2 To update picrust2 PICRUSt2 Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2
pilon 1.20.1 1.24 pilon To update pilon pilon Sequence assembly, Analysis, Read alignment Assembly pilon is a tool for assembly improvement and variant analysis in bacteria Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. To update Variant Analysis pilon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon
pipelign 0.2 0.2 pipelign Up-to-date Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign
pizzly 0.37.3 pizzly To update Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/
plasflow 1.1.0 1.1.0 plasflow Up-to-date PlasFlow - Prediction of plasmid sequences in metagenomic contigs. Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow
plasmidfinder 2.1.6 2.1.6 plasmidfinder Up-to-date PlasmidFinder PlasmidFinder Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers "PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder
plink 1.90b6.21 1.90b6.21 plink Up-to-date plink PLINK Genetic variation analysis GWAS study PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study plink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink
polypolish 0.5.0 0.6.0 polypolish To update Polypolish Polypolish Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping "Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish
porechop 0.2.4 porechop To update Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop
poretools 0.6.1a1 0.6.1a1 poretools Up-to-date poretools Poretools Nucleic acid sequence analysis DNA, Sequencing A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools
presto 0.6.2 0.7.2 presto To update presto pRESTO Nucleic acid sequence analysis Sequencing, DNA, Immunology pRESTO toolkit for immune repertoire analysis. Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. To update https://presto.readthedocs.io/ Sequence Analysis presto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto
pretext 0.0.6 0.0.6 pretextgraph Up-to-date Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext
prinseq @TOOL_VERSION+galaxy2 0.20.4 prinseq To update prinseq PRINSEQ Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets 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. To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/
progressivemauve snapshot_2015_02_13 progressivemauve To update Mauve/ProgressiveMauve Multiple Sequence Aligner To update Sequence Analysis progressivemauve iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve
prokka 1.14.6 1.14.6 prokka Up-to-date prokka Prokka Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Rapid annotation of prokaryotic genomes Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/
prot-scriber 0.1.4 0.1.5 prot-scriber To update Protein annotation of short human readable descriptions To update https://github.com/usadellab/prot-scriber Proteomics prot_scriber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber
proteinortho 6.3.1 6.3.1 proteinortho Up-to-date proteinortho Proteinortho Homology-based gene prediction Phylogeny Proteinortho is a tool to detect orthologous proteins/genes within different species. Proteinortho is a tool to detect orthologous genes within different species Up-to-date https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho
psiclass 1.0.3 1.0.3 psiclass Up-to-date psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass
pureclip 1.0.4 1.3.1 pureclip To update PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip
purge_dups 1.2.6 1.2.6 purge_dups Up-to-date purge_dups purge_dups Genome assembly, Read binning, Scaffolding Sequence assembly Purge haplotigs and overlaps in an assembly based on read depth 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 Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups
pycoqc 2.5.2 2.5.2 pycoqc Up-to-date QC metrics for ONT Basecalling Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc
pyega3 5.0.2 5.1.0 pyega3 To update EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3
pygenometracks 3.8 3.8 pygenometracks Up-to-date pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. Up-to-date https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks
pysradb 1.4.2 2.2.0 pysradb To update pysradb pysradb Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb
qfilt 1.0.0+galaxy1 0.0.1 qfilt To update Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt
qiime_add_on 1.9.1 qiime To update QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
qiime_core 1.9.1 qiime To update QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
qq_tools 0.1.0 0.1.4 r-qqman To update To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis iuc
qualimap 2.2.2d 2.3 qualimap To update qualimap QualiMap Sequencing quality control Data quality management Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. To update http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap
quast 5.2.0 5.2.0 quast Up-to-date quast QUAST Visualisation, Sequence assembly validation Sequence assembly Quast (Quality ASsessment Tool) evaluates genome assemblies. QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast
query_impc 0.9.0 requests To update Contains a tool to query the IMPC database. To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services query_impc iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc
query_tabular 3.3.0 python To update Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular
quickmerge 0.3 0.3 quickmerge Up-to-date quickmerge quickmerge Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Merge long-read and hybrid assemblies to increase contiguity 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. Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge
raceid 0.2.3 0.1.3 r-raceid To update RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3
ragtag 2.1.0 2.1.0 ragtag Up-to-date ragtag ragtag Genome assembly Sequence assembly Reference-guided scaffolding of draft genomes tool. RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Up-to-date https://github.com/malonge/RagTag Assembly ragtag iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag
rapidnj 2.3.2 2.3.2 rapidnj Up-to-date rapidnj RapidNJ Phylogenetic tree generation Phylogeny Galaxy wrapper for the RapidNJ tool A tool for fast canonical neighbor-joining tree construction. Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj
rasusa 0.8.0 0.8.0 rasusa Up-to-date rasusa rasusa Randomly subsample sequencing reads to a specified coverage Produces an unbiased subsample of your reads Up-to-date https://github.com/mbhall88/rasusa Sequence Analysis rasusa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa
raven 1.8.0 1.8.3 raven-assembler To update Raven is a de novo genome assembler for long uncorrected reads. To update https://github.com/lbcb-sci/raven Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven
raxml 8.2.12 8.2.13 raxml To update raxml RAxML Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis RAxML - A Maximum Likelihood based phylogenetic inference A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml
rcorrector 1.0.3+galaxy1 1.0.6 rcorrector To update rcorrector Rcorrector Sequencing error detection RNA, RNA-Seq, Sequencing Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector
read_it_and_keep 0.2.2 0.3.0 read-it-and-keep To update Rapid decontamination of SARS-CoV-2 sequencing reads To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep
recentrifuge 1.14.0 1.14.0 recentrifuge Up-to-date Recentrifuge Recentrifuge Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing "With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." Robust comparative analysis and contamination removal for metagenomics. Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge
red 2018.09.10 2018.09.10 red Up-to-date Red (REpeat Detector) Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red
repeatmasker 4.1.5 4.1.5 repeatmasker Up-to-date repeatmasker RepeatMasker Genome annotation Sequence analysis, Sequence composition, complexity and repeats RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Up-to-date http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker
repeatmodeler 2.0.5 To update RepeatModeler - Model repetitive DNA To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler
repmatch_gff3 matplotlib To update Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. To update ChIP-seq repmatch_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3
reshape2 1.4.2 r-reshape2 To update Flexibly restructure and aggregate data using just the two functions melt and dcast To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2
resize_coordinate_window 1.0.2 python To update Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. To update Genomic Interval Operations resize_coordinate_window iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window
rgcca 3.0.2 3.0.3 rgccacmd To update multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca
rgrnastar 2.7.11a 2.7.11b star To update star STAR Sequence alignment RNA-Seq, Transcriptomics RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper Ultrafast universal RNA-seq data aligner To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar
ribowaltz 1.2.0 2.0 ribowaltz To update riboWaltz riboWaltz Computational biology Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz
rnaquast 2.2.3 2.2.3 rnaquast Up-to-date rnaQUAST rnaQUAST De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. Quality assessment tool for de novo transcriptome assemblies. Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast iuc https://git.ufz.de/lehmanju/rnaquast
roary 3.13.0 3.13.0 roary Up-to-date roary Roary Genome assembly DNA, Genomics, Mapping Roary the pangenome pipeline A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary
rp2biosensor 3.2.1 rp2biosensor To update Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output To update https://github.com/brsynth/rp2biosensor Synthetic Biology rp2biosensor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor
rp2paths 1.5.1 rp2paths To update Enumerate and seperate the different pathways generated by RetroPath2.0 To update https://github.com/brsynth/rp2paths Synthetic Biology rp2paths iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths
rpbasicdesign 1.2.2 rpbasicdesign To update Extracting enzyme IDs from rpSBML files To update https://github.com/brsynth/rpbasicdesign Synthetic Biology rpbasicdesign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign
rpfba 5.12.3 rptools To update Perform FBA for the RetroPath2.0 heterologous pathways To update https://github.com/brsynth/rptools/releases Synthetic Biology rpfba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba
rptools 5.13.1 rptools To update Suite of tools that work on rpSBML format To update https://github.com/brsynth/rptools Synthetic Biology rptools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools
rrparser 2.5.2 rrparser To update Reaction Rules Parser To update https://github.com/brsynth/RRParser Synthetic Biology rrparser iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser
rseqc 5.0.1 5.0.3 rseqc To update rseqc RSeQC Data handling Sequencing an RNA-seq quality control package Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc
ruvseq 1.26.0 1.36.0 bioconductor-ruvseq To update ruvseq RUVSeq Differential gene expression analysis Gene expression, RNA-seq Remove Unwanted Variation from RNA-Seq Data This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq
salsa2 2.3 2.3 salsa2 Up-to-date SALSA SALSA Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping A tool to scaffold long read assemblies with Hi-C > 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 Up-to-date https://github.com/marbl/SALSA Assembly salsa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2
samblaster 0.1.24 0.1.26 samblaster To update samblaster SAMBLASTER Split read mapping DNA, Sequencing, Mapping samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files A tool to mark duplicates and extract discordant and split reads from SAM files. To update https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster
sansa 0.0.8 0.1.1 sansa To update Sansa is a tool for structural variant annotation. To update https://github.com/dellytools/sansa Variant Analysis sansa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa
sarscov2formatter 1.0 1.0 sarscov2formatter Up-to-date sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter
sarscov2summary 0.1 0.5 sarscov2summary To update sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary
sbml2sbol 0.1.13 sbml2sbol To update Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol iuc
scanpy 1.9.6 1.7.2 scanpy To update scanpy SCANPY Differential gene expression analysis Gene expression, Cell biology, Genetics Scanpy – Single-Cell Analysis in Python Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis scanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/
scater 1.22.0 1.30.1 bioconductor-scater To update scater scater Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. To update http://bioconductor.org/packages/scater/ Transcriptomics, RNA, Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater
sceasy 0.0.7 0.0.7 r-sceasy Up-to-date Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Transcriptomics sceasy_convert iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/
schicexplorer 4 7 schicexplorer To update scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization schicexplorer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer
scikit-bio 0.4.2 0.4.2 scikit-bio Up-to-date scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio
scoary 1.6.16 1.6.16 scoary Up-to-date Scoary calculates the assocations between all genes in the accessory genome and the traits. Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary
scpipe 1.0.0+galaxy2 2.2.0 bioconductor-scpipe To update scpipe scPipe Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-seq, Sequencing A flexible preprocessing pipeline for single-cell RNA-sequencing data A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, RNA, Statistics scpipe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe
seacr 1.3 1.3 seacr Up-to-date SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq seacr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr
selenzy_wrapper 0.3.0 0.3.0 selenzy_wrapper Up-to-date Performs enzyme selection from a reaction query. Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology selenzy_wrapper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper
semibin 2.0.2 2.0.2 semibin Up-to-date semibin SemiBin Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Up-to-date https://semibin.readthedocs.io/en/latest/ Metagenomics semibin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin
seq2hla 2.3 2.3 seq2hla Up-to-date seq2hla Seq2HLA Read mapping, Genetic variation analysis Transcriptomics, Mapping Precision HLA typing and expression from RNAseq data seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla
seqcomplexity 0.1.2 0.1.2 seqcomplexity Up-to-date Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/
seqkit 2.3.1 2.7.0 seqkit To update seqkit seqkit DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis A cross-platform and ultrafast toolkit for FASTA/Q file manipulation FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. To update https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit
seqprep 1.3.2 1.3.2 seqprep Up-to-date seqprep SeqPrep Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Tool for merging paired-end Illumina reads and trimming adapters. Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep
seqsero2 1.2.1 1.2.1 seqsero2 Up-to-date Salmonella serotype prediction from genome sequencing data Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2
seqtk 1.4 1.4 seqtk Up-to-date seqtk seqtk Data handling, Sequence file editing Data management Toolkit for processing sequences in FASTA/Q formats A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk
seqwish 0.7.5 0.7.9 seqwish To update Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/
seurat 3.0.2 r-seurat To update A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data To update https://github.com/satijalab/seurat Transcriptomics, RNA, Statistics seurat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat
shasta 0.6.0 0.11.1 shasta To update Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta
shorah 1.1.3 1.99.2 shorah To update shorah ShoRAH Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics Reconstruct haplotypes using ShoRAH in amplicon mode Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah
shovill 1.1.0 1.1.0 shovill Up-to-date shovill shovill Genome assembly Genomics, Microbiology, Sequence assembly Faster de novo assembly pipeline based around Spades 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. Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill
sickle 1.33.2 1.33 sickle-trim To update sickle sickle Sequence trimming Data quality management A windowed adaptive trimming tool for FASTQ files using quality A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle
simtext 0.0.2 1.0.1 r-argparse To update A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext iuc https://github.com/galaxyproject/tools-iuc/tools/simtext
sina 1.7.2 1.7.2 sina Up-to-date sina SINA Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy SINA reference based multiple sequence alignment Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina
sinto 0.9.0 0.10.0 sinto To update Sinto single-cell analysis tools To update https://github.com/timoast/sinto Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto
slamdunk 0.4.3 0.4.3 slamdunk Up-to-date Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk
sleuth 0.30.1 0.30.1 r-sleuth Up-to-date sleuth sleuth Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Sleuth is a program for differential analysis of RNA-Seq data. A statistical model and software application for RNA-seq differential expression analysis. Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth
smallgenomeutilities 0.4.0 0.4.0 smallgenomeutilities Up-to-date v-pipe V-pipe Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Set of utilities for manipulating small viral genome data. Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities
smudgeplot 0.2.5 0.2.5 smudgeplot Up-to-date smudgeplots Smudgeplots Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Inference of ploidy and heterozygosity structure using whole genome sequencing 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 Up-to-date https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot galaxy-australia https://github.com/galaxyproject/tools-iuc
snap 2013_11_29 2013_11_29 snap Up-to-date snap SNAP Gene prediction DNA, DNA polymorphism, Genetics SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap
sniffles 1.0.12 2.2 sniffles To update sniffles Sniffles Sequence analysis, Structural variation detection DNA structural variation, Sequencing Galaxy wrapper for sniffles An algorithm for structural variation detection from third generation sequencing alignment. To update https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles iuc https://github.com/galaxyproject/tools-iuc
snipit 1.2 1.2 snipit Up-to-date snipit snipit Base position variability plotting Virology Summarise snps relative to a reference sequence Summarise snps relative to a reference sequence Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit
snippy 4.6.0 snippy To update snippy snippy Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics Contains the snippy tool for characterising microbial snps Rapid haploid variant calling and core SNP phylogeny generation. To update https://github.com/tseemann/snippy Sequence Analysis snippy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy
snp-dists 0.8.2 0.8.2 snp-dists Up-to-date Compute pairwise SNP distance matrix from a FASTA sequence alignment Up-to-date https://github.com/tseemann/snp-dists Variant Analysis snp_dists iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists
snp-sites 2.5.1 2.5.1 snp-sites Up-to-date Finds SNP sites from a multi-FASTA alignment file Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis snp_sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites
snpeff-covid19 To update snpeff snpEff SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff
snpfreqplot 1.0 r-base To update Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ Variant Analysis snpfreqplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/
socru 2.1.7 2.2.4 socru To update Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru
sonneityping 20210201 20210201 sonneityping Up-to-date Scripts for parsing Mykrobe predict results for Shigella sonnei. Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping
spades 3.15.5 3.15.5 spades Up-to-date biosyntheticspades biosyntheticSPAdes Sequence assembly Sequence assembly, Sequence sites, features and motifs, Genetic engineering 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. biosyntheticSPAdes - biosynthetic gene cluster assembly with paired-end reads Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades
spaln 2.4.9 python To update Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln iuc https://github.com/ogotoh/spaln
spotyping 2.1 2.1 spotyping Up-to-date spotyping SpoTyping Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine
spyboat 0.1.2 spyboat To update Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat
sra-tools 3.0.8 3.0.10 sra-tools To update sra-tools SRA Software Toolkit Data handling DNA, Genomics, Sequencing NCBI Sequence Read Archive toolkit utilities The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. To update https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools
srst2 0.2.0 1.19.2 samtools To update SRST2 Short Read Sequence Typing for Bacterial Pathogens To update http://katholt.github.io/srst2/ Metagenomics srst2 iuc https://github.com/katholt/srst2
stacks 2.65 stacks To update stacks Stacks Data handling Mapping, Population genetics Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks
stacks2 2.55 2.65 stacks To update Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2
star_fusion 0.5.4-3+galaxy1 1.12.0 star-fusion To update STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update Sequence Analysis, Transcriptomics star_fusion iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion
straindesign 3.2.2 3.2.2 straindesign Up-to-date Toolbox to optimize biological model Up-to-date https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign iuc https://github.com/brsynth/straindesign
strelka 2.9.10 2.9.10 strelka Up-to-date Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka
stringtie 2.2.1 2.2.1 stringtie Up-to-date stringtie StringTie Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie
structure 2.3.4 2.3.4 structure Up-to-date structure Structure Genetic variation analysis Population genetics for using multi-locus genotype data to investigate population structure. The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure
structureharvester 0.6.94 0.6.94 structureharvester Up-to-date for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date Phylogenetics, Variant Analysis structureharvester iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester
swift 1.0 1.0 swiftlink Up-to-date Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/
syndiva 1.0 clustalo To update SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA
table_compute 1.2.4 pandas To update Perform general-purpose table operations To update Text Manipulation table_compute iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute
tag_pileup_frequency 1.0.2 openjdk To update Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency
tasmanian_mismatch 1.0.7 1.0.7 tasmanian-mismatch Up-to-date Analysis of positional mismatches Up-to-date Sequence Analysis tasmanian_mismatch iuc https://github.com/nebiolabs/tasmanian-mismatch
taxonomy_filter_refseq 0.3.0 1.0.7 rust-ncbitaxonomy To update Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq iuc https://github.com/galaxyproject/tools-iuc
taxonomy_krona_chart 2.7.1+galaxy0 2.8.1 krona To update krona Krona Visualisation Metagenomics Krona pie chart from taxonomic profile Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart
tb-profiler 4.4.1 5.0.1 tb-profiler To update Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler
tb_variant_filter 0.4.0 0.4.0 tb_variant_filter Up-to-date M. tuberculosis H37Rv VCF filter Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis tb_variant_filter iuc https://github.com/COMBAT-TB/tb_variant_filter
tbl2gff3 1.2 0.6.6 bcbiogff To update Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3
tbvcfreport 0.1.10 0.1.10 tbvcfreport Up-to-date Generate HTML report from SnpEff M.tuberculosis VCF(s) Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis tbvcfreport iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport
te_finder 1.0.1 1.19.2 samtools To update tefinder TEfinder Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation Transposable element insertions finder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/
telescope 1.0.3 1.0.3 telescope Up-to-date Telescope-expression Telescope Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Single locus resolution of Transposable ELEment expression. Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope
tetoolkit 2.2.3 2.2.3 tetranscripts Up-to-date The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit iuc https://github.com/mhammell-laboratory/TEtranscripts
tetyper 1.1 1.1 tetyper Up-to-date Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper
tn93 1.0.6 1.0.13 tn93 To update Compute distances between sequences To update https://github.com/veg/tn93/ Sequence Analysis tn93 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/
tracy 0.6.1 0.7.6 tracy To update To update iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy
transdecoder 5.5.0 5.7.1 transdecoder To update TransDecoder TransDecoder Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing TransDecoder finds coding regions within transcripts TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder
transit 3.0.2 3.2.3 transit To update transit TRANSIT Transposon prediction DNA, Sequencing, Mobile genetic elements TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/
transtermhp 2.09 transtermhp To update Finds rho-independent transcription terminators in bacterial genomes To update Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp
trimmomatic 0.39 0.39 trimmomatic Up-to-date A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic
trinity 2.15.1 2.15.1 trinity Up-to-date trinity Trinity Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity
trinotate 3.2.2 4.0.2 trinotate To update trinotate Trinotate Gene functional annotation Gene expression, Transcriptomics Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate
trycycler 0.5.4 0.5.4 trycycler Up-to-date Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler
tsebra tsebra Up-to-date This tool has been developed to combine BRAKER predictions. Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra
tsne 0.0.2 0.13 r-rtsne To update T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne
tximport 1.22.0 1.30.0 bioconductor-tximport To update tximport tximport Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Wrapper for the Bioconductor package tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. To update http://bioconductor.org/packages/tximport/ Transcriptomics tximport iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport
ucsc_blat 377 445 ucsc-blat To update blat BLAT Sequence alignment Sequence analysis Standalone blat sequence search command line tool Fast, accurate spliced alignment of DNA sequences. To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat yating-l
fasplit 377 377 ucsc-fasplit Up-to-date UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Sequence analysis faSplit is a tool to split a single FASTA file into several files Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit
fatovcf 448 448 ucsc-fatovcf Up-to-date UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Sequence analysis Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_fatovcf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf
twobittofa 377 455 ucsc-twobittofa To update UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Sequence analysis twoBitToFa is a tool to convert all or part of .2bit file to FASTA Utilities for handling sequences and assemblies from the UCSC Genome Browser project. To update https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats ucsc_twobittofa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa
wigtobigwig 447 447 ucsc-wigtobigwig Up-to-date UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Sequence analysis converts bedGraph (wig) files into binary bigwig Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats ucsc_wigtobigwig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig
umi_tools 1.1.2 1.1.5 umi_tools To update umi-tools UMI-tools Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs UMI-tools extract - Extract UMIs from fastq Tools for handling Unique Molecular Identifiers in NGS data sets. To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools
unicycler 0.5.0 0.5.0 unicycler Up-to-date unicycler Unicycler Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Unicycler is a hybrid assembly pipeline for bacterial genomes. A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler
usher 0.2.1 0.6.3 usher To update UShER toolkit wrappers To update https://github.com/yatisht/usher Phylogenetics usher iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher
valet 1.0 valet To update A pipeline for detecting mis-assemblies in metagenomic assemblies. To update https://github.com/marbl/VALET Metagenomics valet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet
vapor 1.0.2 1.0.2 vapor Up-to-date vapor VAPOR Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Classify Influenza samples from raw short read sequence data VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor
vardict 1.8.3 python To update VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict
variant_analyzer 2.0.0 matplotlib To update Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer
varscan 2.4.3 2.4.6 varscan To update VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan
varvamp 1.1.1 1.1.1 varvamp Up-to-date varvamp varVAMP PCR primer design Virology Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP
vcf2maf 1.6.21 1.6.21 vcf2maf Up-to-date vcf2maf: Convert VCF into MAF Up-to-date Convert Formats vcf2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf
vcfanno 0.3.5 0.3.5 vcfanno Up-to-date vcfanno vcfanno SNP annotation Genetic variation, Data submission, annotation and curation Annotate VCF files Fast, flexible annotation of genetic variants. Up-to-date https://github.com/brentp/vcfanno Variant Analysis vcfanno iuc https://github.com/galaxyproject/tools-iuc/vcfanno/
vegan 2.4-3 2.3_4 r-vegan To update To update https://cran.r-project.org/package=vegan Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/
velocyto 0.17.17 0.17.17 velocyto.py Up-to-date Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics velocyto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto
velvet 1.2.10 velvet To update velvet Velvet Formatting, De-novo assembly Sequence assembly de novo genomic assembler specially designed for short read sequencing technologies A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet
velvet_optimiser 2.2.6+galaxy2 1.2.10 velvet To update velvetoptimiser VelvetOptimiser Optimisation and refinement, Sequence assembly Genomics, Sequence assembly Automatically optimize Velvet assemblies This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser
verkko 1.3.1 2.0 verkko To update Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko
vg 1.23.0 1.55.0 vg To update Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg
virhunter 1.0.0 numpy To update virhunter VirHunter Sequence classification Virology Deep Learning method for novel virus detection in sequencing data VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). To update https://github.com/cbib/virhunter Machine Learning virhunter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter
volcanoplot 0.0.5 2.2.1 r-ggplot2 To update Tool to create a Volcano Plot To update Visualization, Transcriptomics, Statistics volcanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot
vsearch 2.8.3 2.27.0 vsearch To update vsearch VSEARCH DNA mapping, Chimera detection Metagenomics, Sequence analysis VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. To update https://github.com/torognes/vsearch Sequence Analysis vsearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch
vsnp 3.0.6 0.22.0 pysam To update The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp
weather_app 0.1.2 curl To update provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app
weblogo3 3.5.0 3.7.9 weblogo To update weblogo WebLogo Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis Sequence Logo generator for fasta Web-based application designed to make generate sequence logos. To update Graphics weblogo3 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3
windowmasker 1.0 2.15.0 blast To update Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/
winnowmap 2.03 2.03 winnowmap Up-to-date A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers winnowmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap
xpath 1.47 perl-xml-xpath To update XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath
yahs 1.2a.2 1.2a.2 yahs Up-to-date Yet Another Hi-C scaffolding tool Up-to-date https://github.com/c-zhou/yahs Assembly yahs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs
zerone 1.0 1.0 zerone Up-to-date ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone
bamtools 2.5.2 2.5.2 bamtools Up-to-date Operate on and transform BAM datasets in various ways using bamtools Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools
bamtools_filter 2.5.2 2.5.2 bamtools Up-to-date Filter BAM datasets on various attributes using bamtools filter Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter
bamtools_split 2.5.2 2.5.2 bamtools Up-to-date Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split
biotradis 1.4.5 1.4.5 biotradis Up-to-date Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis
cuffcompare 2.2.1 2.2.1 cufflinks Up-to-date Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare
cuffdiff 2.2.1 2.2.1 cufflinks Up-to-date Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff
cufflinks 2.2.1 2.2.1 cufflinks Up-to-date Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks
cuffmerge 2.2.1 2.2.1 cufflinks Up-to-date Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge
cuffnorm 2.2.1 2.2.1 cufflinks Up-to-date The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm
cuffquant 2.2.1 2.2.1 cufflinks Up-to-date The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant
fasta_clipping_histogram 0.0.14 0.0.14 fastx_toolkit Up-to-date Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram
fasta_formatter 0.0.14 0.0.14 fastx_toolkit Up-to-date FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter
fasta_nucleotide_changer 0.0.14 0.0.14 fastx_toolkit Up-to-date RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer
fastq_quality_boxplot 0.0.14 0.0.14 fastx_toolkit Up-to-date Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot
fastq_quality_converter 0.0.14 0.0.14 fastx_toolkit Up-to-date Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter
fastq_quality_filter 0.0.14 0.0.14 fastx_toolkit Up-to-date Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter
fastq_to_fasta 0.0.14 0.0.14 fastx_toolkit Up-to-date FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta
fastx_artifacts_filter 0.0.14 0.0.14 fastx_toolkit Up-to-date Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter
fastx_barcode_splitter 0.0.14 0.0.14 fastx_toolkit Up-to-date Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter
fastx_clipper 0.0.14 0.0.14 fastx_toolkit Up-to-date Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper
fastx_collapser 0.0.14 0.0.14 fastx_toolkit Up-to-date Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser
fastx_nucleotides_distribution 0.0.14 0.0.14 fastx_toolkit Up-to-date Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution
fastx_quality_statistics 0.0.14 0.0.14 fastx_toolkit Up-to-date Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics
fastx_renamer 0.0.14 0.0.14 fastx_toolkit Up-to-date Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer
fastx_reverse_complement 0.0.14 0.0.14 fastx_toolkit Up-to-date Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement
fastx_trimmer 0.0.14 0.0.14 fastx_toolkit Up-to-date Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer
fastq_combiner 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date Combine FASTA and QUAL into FASTQ Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner
fastq_filter 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date Filter FASTQ reads by quality score and length Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter
fastq_groomer 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date Convert between various FASTQ quality formats. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer
fastq_manipulation 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date Manipulate FASTQ reads on various attributes. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation
fastq_masker_by_quality 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date FASTQ Masker by quality score Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality
fastq_paired_end_deinterlacer 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date FASTQ de-interlacer on paired end reads. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer
fastq_paired_end_interlacer 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date FASTQ interlacer on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer
fastq_paired_end_joiner 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date FASTQ joiner on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner
fastq_paired_end_splitter 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date FASTQ splitter on joined paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter
fastq_stats 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date FASTQ Summary Statistics by column Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats
fastq_to_tabular 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date FASTQ to Tabular converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular
fastq_trimmer 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date FASTQ Trimmer by quality Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer
fastqtofasta 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date FASTQ to FASTA converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta
tabular_to_fastq 1.1.5 1.1.5 galaxy_sequence_utils Up-to-date Tabular to FASTQ converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq
kraken 1.1.1 kraken To update Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/
kraken2 2.1.1 2.1.3 kraken2 To update kraken2 kraken2 Taxonomic classification Taxonomy, Metagenomics Kraken2 for taxonomic designation. 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. To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/
samtools 1.15.1 1.19.2 samtools To update To update https://github.com/samtools/samtools SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools
snpeff 1.70 biopython To update SnpEff is a genetic variant annotation and effect prediction toolbox To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff
snpsift 5.2 snpsift To update snpEff SnpSift tools from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis snpsift iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift
snpsift_dbnsfp 5.2 snpsift To update snpEff SnpSift dbnsfp tool from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis snpsift_dbnsfp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp
snpsift_genesets 5.2 snpsift To update Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/
vcf2tsv 1.0.9 vcflib To update Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv
vcfaddinfo 1.0.9 vcflib To update Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo
vcfallelicprimitives 1.0.9 vcflib To update Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives
vcfannotate 1.0.9 vcflib To update Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate
vcfannotategenotypes 1.0.9 vcflib To update Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes
vcfbedintersect 1.0.9 vcflib To update Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect
vcfbreakcreatemulti 1.0.9 vcflib To update Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti
vcfcheck 1.0.9 vcflib To update Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck
vcfcombine 1.0.9 vcflib To update Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine
vcfcommonsamples 1.0.9 vcflib To update Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples
vcfdistance 1.0.9 vcflib To update Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance
vcffilter 1.0.9 vcflib To update Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter
vcffixup 1.0.9 vcflib To update Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup
vcfflatten 1.0.9 vcflib To update Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten
vcfgeno2haplo 1.0.9 vcflib To update Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo
vcfgenotypes 1.0.9 vcflib To update Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes
vcfhethom 1.0.9 vcflib To update Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom
vcfleftalign 1.0.9 vcflib To update Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign
vcfprimers 1.0.9 vcflib To update Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers
vcfrandomsample 1.0.9 vcflib To update Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample
vcfselectsamples 1.0.9 vcflib To update Select samples from a VCF file To update https://github.com/ekg/vcflib Variant Analysis vcfselectsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples
vcfsort 1.0.9 vcflib To update Sort VCF dataset by coordinate To update https://github.com/ekg/vcflib Variant Analysis vcfsort devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort
vcfvcfintersect 1.0.9 vcflib To update Intersect two VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfvcfintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect
ThermoRawFileParser 1.3.4 1.4.3 thermorawfileparser To update Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser
appendfdr 0.2.0 To update To update appendfdr galaxyp
bed_to_protein_map 0.2.0 python To update Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map
blast_plus_remote_blastp 2.6.0 2.15.0 blast To update NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus
bumbershoot 3.0.21142 3_0_21142_0e4f4a4 bumbershoot To update To update http://proteowizard.sourceforge.net/ Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
calisp 3.0.13 3.0.13 calisp Up-to-date Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp
cardinal 2.10.0 3.4.3 bioconductor-cardinal To update Statistical and computational tools for analyzing mass spectrometry imaging datasets To update http://cardinalmsi.org Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal
dbbuilder 0.3.4 wget To update Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder
decoyfasta To update Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta
dia_umpire 2.1.3 2.1.6 dia_umpire To update DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire
dialignr 1.2.0 2.10.0 bioconductor-dialignr To update DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr
diann 1.8.1 To update DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann galaxyp https://github.com/vdemichev/DiaNN
diapysef 1.0.10 diapysef To update diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef
diffacto 1.0.6 1.0.6 diffacto Up-to-date Diffacto comparative protein abundance estimation Up-to-date https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto
digestdb 0.1.0 trans_proteomic_pipeline To update To update digestdb galaxyp
directag_and_tagrecon To update To update directag_and_tagrecon galaxyp
data_manager_eggnog_mapper To update downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager
data_manager_eggnog_mapper_abspath To update download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath
eggnog_mapper 2.1.8 2.1.12 eggnog-mapper To update eggnog-mapper-v2 eggNOG-mapper v2 Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis eggnog-mapper fast functional annotation of novel sequences EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper
encyclopedia 1.12.34 2.12.30 encyclopedia To update Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia
fasta_merge_files_and_filter_unique_sequences 1.2.0 python To update Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences
fastg2protlib 1.0.2 To update Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib
feature_alignment 0.11.0 0.11.0 msproteomicstools Up-to-date TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md
filter_by_fasta_ids 2.3 python To update Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids
flashlfq 1.2.6 flashlfq To update FlashLFQ mass-spectrometry proteomics label-free quantification To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq
gffcompare_to_bed 0.2.1 python To update Filter and convert a gffCompare GTF to BED To update https://github.com/gpertea/gffcompare/ Convert Formats gffcompare_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed
hardklor 2.30.1+galaxy1 2.3.2 hardklor To update Hardklör To update Proteomics hardklor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor
idconvert 3_0_9992 proteowizard To update Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
lfq_protein_quant 1.0 2.28.1 bioconductor-msnbase To update Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant
ltq_iquant_cli To update To update ltq_iquant_cli galaxyp
maldiquant 1.22.0 r-base To update MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant
map_peptides_to_bed 0.2 1.70 biopython To update Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed
maxquant maxquant Up-to-date wrapper for MaxQuant Up-to-date https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant Proteomics maxquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant
meta_proteome_analyzer 2.0.0 2.0.0 mpa-portable Up-to-date MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer
metagene_annotator 1.0.0 1.0 metagene_annotator To update MetaGeneAnnotator gene-finding program for prokaryote and phage To update Sequence Analysis metagene_annotator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator
metanovo 1.9.4 1.9.4 metanovo Up-to-date Produce targeted databases for mass spectrometry analysis. Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo
metaquantome 2.0.2 2.0.2 metaquantome Up-to-date quantitative analysis of microbiome taxonomy and function Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome
mgf_formatter 1.0.0 1.0.0 mgf-formatter Up-to-date Up-to-date mgf_formatter galaxyp
moFF 2.0.3 2.0.3 moff Up-to-date moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF
morpheus 2.255.0 287 morpheus To update Morpheus MS Search Application To update Proteomics morpheus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus
mqppep 0.1.19 1.64.0 bioconductor-preprocesscore To update MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep
msconvert 3.0.20287 To update msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container To update Proteomics msconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
msgfplus 0.5 2023.01.1202 msgf_plus To update MSGF+ To update Proteomics msgfplus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus
msms_extractor 1.0.0 3_0_9992 proteowizard To update Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor galaxyp
msstats 4.0.0 4.10.0 bioconductor-msstats To update MSstats tool for analyzing mass spectrometry proteomic datasets To update https://github.com/MeenaChoi/MSstats Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats
msstatstmt 2.0.0 2.10.0 bioconductor-msstatstmt To update MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt
mt2mq 1.1.0 r-tidyverse To update Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq galaxyp
mz_to_sqlite 2.1.1+galaxy0 2.1.1 mztosqlite To update Creates a SQLite database for proteomics data To update Proteomics mz_to_sqlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite
openms 2.8 3.1.0 openms To update OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms
pathwaymatcher 1.9.1 pathwaymatcher To update Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher
pep_pointer 0.1.3+galaxy1 python To update PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer
pepquery 1.6.2 2.0.2 pepquery To update A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery
pepquery2 2.0.2 2.0.2 pepquery Up-to-date PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2
peptide_genomic_coordinate 1.0.0 python To update Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate galaxyp
peptideshaker 4.3.6 searchgui To update PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker
pepxml_to_xls To update Convert PepXML to Tabular To update Proteomics pepxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls
percolator 3.5 3.5 percolator Up-to-date Percolator Up-to-date Proteomics percolator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator
pi_db_tools 1.3 python To update HiRIEF tools To update Proteomics hirieftools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools
pmd_fdr 1.4.0 r-base To update Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr
custom_pro_db 1.22.0 1.37.1 bioconductor-rgalaxy To update CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db
custom_pro_db_annotation_data_manager To update CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db
psm2sam r-base To update PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam
proteinpilot 0.1 To update To update proteinpilot galaxyp
retrieve_ensembl_bed 0.1.0 To update Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed
translate_bed 0.1.0 To update Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed
proteomiqon_joinquantpepionswithproteins 0.0.1 0.0.2 proteomiqon-joinquantpepionswithproteins To update The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins
proteomiqon_labeledproteinquantification 0.0.1 0.0.3 proteomiqon-labeledproteinquantification To update The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification
proteomiqon_labelfreeproteinquantification 0.0.1 0.0.3 proteomiqon-labelfreeproteinquantification To update The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification
proteomiqon_mzmltomzlite 0.0.8 0.0.8 proteomiqon-mzmltomzlite Up-to-date The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite
proteomiqon_peptidedb 0.0.7 0.0.7 proteomiqon-peptidedb Up-to-date The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb
proteomiqon_peptidespectrummatching 0.0.7 0.0.7 proteomiqon-peptidespectrummatching Up-to-date Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching
proteomiqon_proteininference 0.0.7 0.0.7 proteomiqon-proteininference Up-to-date MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference
proteomiqon_psmbasedquantification 0.0.8 0.0.9 proteomiqon-psmbasedquantification To update The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification
proteomiqon_psmstatistics 0.0.8 0.0.8 proteomiqon-psmstatistics Up-to-date The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics
proteore_venn_diagram 2021.06.08 python To update ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram galaxyp
protxml_to_xls 0.1.0 trans_proteomic_pipeline To update To update protxml_to_xls galaxyp
psm_eval 0.1.0 binaries_for_psm_eval To update To update psm_eval galaxyp
psm_validation 1.0.3 To update Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation
pyprophet 2.1.4 2.2.5 pyprophet To update Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet
pyteomics 4.4.1 4.7.1 pyteomics To update pyteomics Pyteomics Protein identification Proteomics, Proteomics experiment Tools using the pyteomics library Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics
quantp 1.1.2 1.11.6 r-data.table To update Correlation between protein and transcript abundance To update Proteomics quantp galaxyp
quantwiz_iq 2.0 2.0 quantwiz-iq Up-to-date Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq
qupath_roi_splitter 0.1.0+galaxy1 geojson To update Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter galaxyp hhttps://github.com/npinter/ROIsplitter
rawtools 2.0.4 rawtools To update Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools
regex_find_replace 1.0.3 python To update Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace
scaffold 0.1.0 scaffold To update To update scaffold galaxyp
sixgill 0.2.4 0.2.4 sixgill Up-to-date Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill
spectrast2spectrast_irt 0.1.0 0.11.0 msproteomicstools To update Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt
spectrast2tsv 0.1.0 0.11.0 msproteomicstools To update Filter from spectraST files to swath input files To update Proteomics spectrast2tsv galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv
translate_bed_sequences 0.2.0 1.70 biopython To update Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences
unipept 4.5.1 python To update Unipept retrieves metaproteomics information To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept galaxyp https://unipept.ugent.be/apidocs
uniprotxml_downloader 2.4.0 requests To update Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader
validate_fasta_database 0.1.5 1.0 validate-fasta-database To update runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database galaxyp
bio3d 2.4_1 2.3_3 r-bio3d To update Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d
biomoldyn 1.5.2 scipy To update Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
ambertools 21.10 ambertools To update Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
packmol 18.169.1 packmol To update PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem
topologyeditors 0 python To update Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors
free_energy To update Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy
gromacs 2022 2021.3 gromacs To update GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs
mdanalysis 1.0.0 mdanalysis To update MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
mdfileconverter 1.9.7 mdtraj To update A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter
mdslicer 1.9.9 mdtraj To update A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer
mdtraj 1.9.7 mdtraj To update MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
openmm 1.8.1 pdbfixer To update OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm
vmd To update vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd
artbio_bam_cleaning 1.10+galaxy0 1.19.2 samtools To update filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning
bamparse 4.1.1 0.22.0 pysam To update Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse
bigwig_to_bedgraph 377+galaxy1 448 ucsc-bigwigtobedgraph To update Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph
bigwig_to_wig 3+galaxy0 377 ucsc-bigwiginfo To update Converts a bigWig file to Wiggle (WIG) format To update https://artbio.fr Convert Formats bigwig_to_wig artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig
blast_to_scaffold 1.1.0 python To update Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold
blast_unmatched 1.0.1 python To update Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched
blastparser_and_hits 2.7.1 python To update Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits
blastx_to_scaffold 1.1.1 python To update Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold
cap3 2.0.1 10.2011 cap3 To update cap3 wrapper To update http://artbio.fr Assembly cap3 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3
cherry_pick_fasta 4.1 python To update Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta
concat_multi_datasets 1.4.2 To update Concatenate multiple datasets tail-to-head, including collection datasets. To update http://artbio.fr Text Manipulation concatenate_multiple_datasets artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets
cpm_tpm_rpk 0.5.2 1.3.2 r-optparse To update Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk
deseq2_normalization 1.40.2+galaxy0 1.42.0 bioconductor-deseq2 To update Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization
embl2fa 0.2 To update Converts EMBL flat format to fasta format To update http://artbio.fr Text Manipulation embl2fa artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa
ez_histograms 3.4.4 2.2.1 r-ggplot2 To update ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms
fetch_fasta_from_ncbi 3.1.0 1.12 urllib3 To update Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi
fisher_test 2.32.0+galaxy0 2.34.0 bioconductor-qvalue To update Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test
gatk4 gatk4 To update Find somatic variations To update http://artbio.fr Variant Analysis gatk4 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4
get_reference_fasta 0.3.2 To update Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta
gsc_center_scale 4.3.1+galaxy0 1.3.2 r-optparse To update Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale
gsc_filter_cells 4.3.1+galaxy0 1.3.2 r-optparse To update Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells
gsc_filter_genes 4.3.1+galaxy0 1.3.2 r-optparse To update Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes
gsc_gene_expression_correlations 4.3.1+galaxy0 1.3.2 r-optparse To update Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations
gsc_high_dimensions_visualisation 4.3+galaxy0 1.3.2 r-optparse To update Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization
gsc_mannwhitney_de 4.1.3+galaxy0 1.3.2 r-optparse To update Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de
gsc_scran_normalize 1.28.1+galaxy0 1.30.0 bioconductor-scran To update Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize
gsc_signature_score 2.3.9+galaxy0 1.3.2 r-optparse To update Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score
guppy 0.2.2 To update A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy
high_dim_heatmap 3.1.3+galaxy0 2.17.0 r-gplots To update gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap
justdiff 3.10+galaxy0 diffutils To update Unix diff To update http://artbio.fr Text Manipulation justdiff artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff
justgzip 2.8+galaxy0 pigz To update Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip
lumpy_smoove 0.2.8+galaxy1 0.7.1 svtyper To update Galaxy wrapper of the lumpy-using smoove workflow To update http://artbio.fr Variant Analysis lumpy_smoove artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove
manta 1.6 1.6.0 manta To update Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta
mapping_quality_stats 0.22.0 1.3.2 r-optparse To update Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats
mircounts 1.6 tar To update Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts
mutational_patterns 3.12.0 3.12.0 bioconductor-mutationalpatterns Up-to-date Mutational patterns and signatures in base substitution catalogs Up-to-date http://artbio.fr Variant Analysis mutational_patterns artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns
oases 1.4.0 0.2.09 oases To update Short read assembler To update http://artbio.fr Assembly, RNA oases artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases
pathifier 1.40.0 1.40.0 bioconductor-pathifier Up-to-date pathifier Up-to-date https:// Transcriptomics, Statistics pathifier artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier
pindel 0.2.5b9 0.2.5b9 pindel Up-to-date Pindel detects genome-wide structural variation. Up-to-date http://artbio.fr Variant Analysis pindel artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel
probecoverage 0.22.0 0.22.0 pysam Up-to-date computes and plots read coverage of genomic regions by sequencing datasets Up-to-date http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage
repenrich 1.5.2 4.0.2 bioconductor-edger To update Repeat element profiling To update https://github.com/nskvir/RepEnrich Transcriptomics, Variant Analysis repenrich artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich
rsem 1.3.3 rsem To update transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem
sambamba 0.7.1+galaxy1 1.0 sambamba To update filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM To update http://artbio.fr SAM sambamba artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba
sashimi_plot 0.1.1 python To update Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot
sequence_format_converter 2.2.0 python To update various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter
small_rna_clusters 1.3.0 0.22.0 pysam To update clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters
small_rna_maps 3.1.1 numpy To update Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps
small_rna_signatures 3.4.2 0.22.0 pysam To update Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures
snvtocnv 3.0.0+galaxy1 3.0.0 sequenza-utils To update infer copy number variations from a vcf file with SNVs using R sequenza To update http://artbio.fr Variant Analysis snvtocnv artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv
sr_bowtie 2.3.0 1.3.1 bowtie To update bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie
sr_bowtie_dataset_annotation 2.8 1.3.1 bowtie To update Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation
tarfast5 0.6.1 pigz To update produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5
varscan_vaf 0.1 python To update Compute variant allele frequency in vcf files generated by varscan. To update http://artbio.fr Variant Analysis varscan_vaf artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf
xpore 2.1+galaxy0 2.1 xpore To update Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore
yac_clipper 2.5.1 python To update Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper
EMLassemblyline 0.1.1+galaxy0 r-emlassemblyline To update Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline
Ecoregionalization_workflow 0.1.0+galaxy0 r-base To update Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow
Geom_mean_workflow 0.1.0+galaxy0 r-base To update 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). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow
PAMPA 0.0.2 To update Tools to compute and analyse biodiversity metrics To update Ecology pampa ecology https://github.com/ColineRoyaux/PAMPA-Galaxy
ab1_fastq 1.20.0 1.38.0 bioconductor-sangerseqr To update Tool to convert ab1 files into FASTQ files To update Convert Formats ab1fastq ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq
champ_blocs 0.0.0 r-base To update Compute indicators for turnover boulders fields To update Ecology ecology https://github.com/Marie59/champ_blocs
consensus_from_alignments 1.0.0 r-bioseq To update Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments
data_exploration 0.0.0 r-tangles To update Explore data through multiple statistical tools To update Ecology ecology https://github.com/Marie59/Data_explo_tools
xarray 2022.3.0 xarray To update xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/
gdal 3.0.0 To update Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal
interpolation 1.0 r-getopt To update Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation
medenv 0.0.1 pandas To update Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source ecology https://github.com/jeremyfix/medenv
obisindicators 0.0.2 r-base To update Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators
ocean 0.1.15 To update Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean
regionalgam 1.5 r-mgcv To update To update https://github.com/RetoSchmucki/regionalGAM Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam
spocc 1.2.2 To update Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc
srs_tools 0.0.1 r-base To update Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology ecology https://github.com/Marie59/Sentinel_2A/srs_tools
stoc 0.0.2 To update Tools to analyse STOC data. To update Ecology stoceps ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc
vigiechiro 0.1.1 To update Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro
xmlstarlet 1.6.1 xmlstarlet To update Tool to convert a xml file from one metadata standard to another To update Convert Formats xmlstarlet ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet
c3s 0.2.0 python To update Copernicus Climate Change Service (C3S) To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis c3s climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s
cads 0.1.0 python To update Copernicus Atmosphere Data Store (ADS) To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis cads climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads
cdo 2.0.0 To update CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo
cesm 2.1.3 2.1.3 cesm Up-to-date Community Earth System Model (CESM) Up-to-date https://www.cesm.ucar.edu/ Climate Analysis cesm climate https://github.com/ESCOMP/CESM
climate-stripes 1.0.2 python To update Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes
eodie 1.0.2 eodie To update Earth Observation Data Information Extractor To update https://eodie.readthedocs.io/ Climate Analysis eodie climate https://gitlab.com/eetun-tiimi/EODIE
essential_climate_variables 0.2.0 python To update Get Copernicus Essential Climate Variables for assessing climate variability To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source cds_essential_variability climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables
fates-emerald 2.0 fates-emerald To update EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis ctsm_fates climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald
mean-per-zone 0.2.0 python To update Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone
psy-maps 1.2.1 python To update Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps
shift-longitudes 0.1.0 python To update Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis shift_longitudes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes
smithsonian-volcanoes 0.1.0 python To update Retrieve data from Volcanoes of the World (VOTW) Database To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data smithsonian_volcanoes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes
droplet-barcode-plot 1.6.1+galaxy2 0.0.1 scxa-plots To update Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml
fastq_provider 0.4.4 0.4.7 atlas-fastq-provider To update Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider
gtf-2-gene-list 1.52.0+galaxy0 1.1.0 atlas-gene-annotation-manipulation To update Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml
fastq_pair 1.0+galaxy0 1.0 fastq-pair To update Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair
fastq_quality_trimmer 0.0.14+galaxy0 0.0.14 fastx_toolkit To update FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer
fastq_utils 0.25.1+galaxy0 0.25.2 fastq_utils To update Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils
salmon-kallisto-mtx-to-10x 0.0.1+galaxy6 scipy To update Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml
cell-types-analysis 1.1.1 0.1.11 cell-types-analysis To update Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
data-hca v0.0.4+galaxy0 0.0.4 hca-matrix-downloader To update Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
data-scxa v0.0.2+galaxy2 wget To update Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
decoupler 1.4.0+galaxy1 1.5.0 decoupler To update decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
dropletutils 1.0.4 0.0.5 dropletutils-scripts To update De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
garnett 0.2.8 0.0.5 garnett-cli To update De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
monocle3 0.1.4 0.0.9 monocle3-cli To update De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
sc3 1.8.0 0.0.6 sc3-scripts To update De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
scanpy 1.9.3 1.9.301 scanpy-scripts To update scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy
scater 1.10.0 0.0.5 scater-scripts To update De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
sccaf 0.0.9 0.0.10 sccaf To update SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf
sceasy 0.0.5 0.0.7 r-sceasy To update Convert scRNA data object between popular formats To update Transcriptomics sceasy ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
scmap 1.6.3 0.1.0 scmap-cli To update De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
scpred 1.0.2 0.1.0 scpred-cli To update De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/
seurat 4.0.0 4.0.0 seurat-scripts Up-to-date De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 Up-to-date https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa
ucsc-cell-browser 1.0.0+galaxy1 1.2.5 ucsc-cell-browser To update Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml
biotransformer 3.0.20230403 3.0.20230403 biotransformer Up-to-date biotransformer BioTransformer Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR BioTransformer is a tool for prediction of small molecule metabolism in mammals. BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer
filter_compounds 3.1.1 2.3.90dev7d621d9 openbabel To update Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds
matchms 0.24.0 0.24.2 matchms To update matchms Matchms Spectral library search, Format validation, Filtering Metabolomics Searching, filtering and converting mass spectral libraries. Tool to import, process, clean, and compare mass spectrometry data. To update https://github.com/matchms/matchms Metabolomics matchms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms
misc 1.0.0 To update To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc
msmetaenhancer 0.3.0 0.3.0 msmetaenhancer Up-to-date msmetaenhancer MSMetaEnhancer Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Tool for mass spectra metadata annotation. Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer
msp_merge 0.1.0 0.24.2 matchms To update To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge
mzml_validator 0.1.0+galaxy2 lxml To update mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator
qcxms 5.2.1 To update QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). To update https://github.com/grimme-lab/QCxMS Computational chemistry, Molecular Dynamics QCxMS recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms
query 0.2 click To update Execute an SQL statement on a set of tables To update Text Manipulation query recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query
ramclustr 1.3.0 1.3.1 r-ramclustr To update ramclustr RAMClustR Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. To update https://rdrr.io/cran/RAMClustR/ Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr
recetox_aplcms 0.12.0 0.12.0 r-recetox-aplcms Up-to-date recetox-aplcms recetox-aplcms Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Peak detection tool for HRMS profile data. recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms
recetox_msfinder v3.5.2 To update recetox-msfinder recetox-msfinder Annotation Metabolomics This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. To update https://github.com/RECETOX/recetox-msfinder Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder
recetox_xmsannotator 0.10.0 0.10.0 r-recetox-xmsannotator Up-to-date recetox-xmsannotator recetox-xMSannotator Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator
rem_complex 1.0.0 pandas To update Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex
retip 0.5.4 To update retip Retip Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. To update https://github.com/PaoloBnn/Retip Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip
riassigner 0.4.0 0.4.0 riassigner Up-to-date riassigner RIAssigner Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner
rmassbank 3.0.0 python To update RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank
spec2vec 0.8.0 0.8.0 spec2vec Up-to-date spec2vec Spec2Vec Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Mass spectra similarity scoring using a trained Spec2Vec model. Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec
waveica 0.2.0 0.2.0 r-recetox-waveica Up-to-date waveica WaveICA Standardisation and normalisation Metabolomics Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Up-to-date https://github.com/RECETOX/WaveICA Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica
xtb 6.6.1 xtb To update Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb
consolidate_vcfs 1.8.2 1.8.2 snvphyl-tools Up-to-date Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs nml https://github.com/phac-nml/snvphyl-galaxy
filter_density 1.8.2 1.8.2 snvphyl-tools Up-to-date Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density nml https://github.com/phac-nml/snvphyl-galaxy
filter_stats 1.8.2 1.8.2 snvphyl-tools Up-to-date SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats nml https://github.com/phac-nml/snvphyl-galaxy
filter_vcf 1.8.2 1.8.2 snvphyl-tools Up-to-date SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf nml https://github.com/phac-nml/snvphyl-galaxy
find_repeats 1.8.2 1.8.2 snvphyl-tools Up-to-date Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats nml https://github.com/phac-nml/snvphyl-galaxy
positions2snv_alignment 1.8.2 1.8.2 snvphyl-tools Up-to-date Generate alignment of SNVs from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_alignment nml https://github.com/phac-nml/snvphyl-galaxy
positions2snv_invariant_alignment 1.8.2 1.8.2 snvphyl-tools Up-to-date Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_invariant_alignment nml https://github.com/phac-nml/snvphyl-galaxy
snv_matrix 1.8.2 1.8.2 snvphyl-tools Up-to-date Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix nml https://github.com/phac-nml/snvphyl-galaxy
vcf2snvalignment 1.8.2 1.8.2 snvphyl-tools Up-to-date Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment nml https://github.com/phac-nml/snvphyl-galaxy
verify_map 1.8.2 1.8.2 snvphyl-tools Up-to-date Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map nml https://github.com/phac-nml/snvphyl-galaxy
suite_snvphyl To update SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 nml https://github.com/phac-nml/snvphyl-galaxy
cooler 0.9.3 1.19.1 htslib To update cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml
fromHicupToJuicebox 0.0.2 0.22.0 pysam To update Convert the output of hicup (as sam or bam) to the input of juicebox. To update Epigenetics from_hicup_to_juicebox lldelisle
fromgtfTobed12 0.11.1+galaxy1 0.12 gffutils To update Convert GTF files to BED12 format To update https://pythonhosted.org/gffutils/contents.html Convert Formats fromgtftobed12 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12
getTn5ExtendedCoverage 0.0.2 0.22.0 pysam To update Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension To update Epigenetics gettn5extendedcoverage lldelisle
hyperstack_to_bleach_corrected_movie 20230328 20231211 Fiji To update Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie
incucyte_stack_and_upload_omero 20231221 20231211 Fiji To update Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero
measure_gastruloids 20221216 20231211 fiji To update Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids
omero_clean_rois_tables 20230623 20231211 fiji To update Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables
omero_get_children_ids 0.1.0 5.11.1 omero-py To update Get omero id of children of an omero object id To update Imaging omero_get_children_ids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids
omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 20231211 fiji To update Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid
omero_hyperstack_to_gastruloid_measurements 20240214 20231211 fiji To update Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements
revertR2orientationInBam 0.0.2 1.19.2 samtools To update Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam
upload_roi_and_measures_to_omero 0.0.5 5.11.1 omero-py To update Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero
blast2go 0.0.11 b2g4pipe To update Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go
blast_rbh 0.3.0 1.70 biopython To update BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
blastxml_to_top_descr 0.1.2 python To update Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr
make_nr 0.0.2 1.70 biopython To update Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr
ncbi_blast_plus 2.14.1 python To update NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus