diff --git a/results/all_tools_wordcloud.png b/results/all_tools_wordcloud.png new file mode 100644 index 00000000..29957922 Binary files /dev/null and b/results/all_tools_wordcloud.png differ diff --git a/results/imaging/index.html b/results/imaging/index.html new file mode 100644 index 00000000..0d989b1f --- /dev/null +++ b/results/imaging/index.html @@ -0,0 +1,143 @@ + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ExpandGalaxy wrapper idGalaxy wrapper versionConda versionConda idStatusbio.tool idbio.tool nameEDAM operationEDAM topicDescriptionbio.tool descriptionStatusSourceToolShed categoriesToolShed idGalaxy wrapper ownerGalaxy wrapper source
imagecoordinates_flipaxis0.1-2pandasTo updategalaxy_image_analysisGalaxy Image AnalysisImage analysisImaging, BioinformaticsFlip coordinate axesDeveloped within the Biomedical Computer Vision (BMCV) Group Heidelberg.To updatehttps://github.com/bmcvImagingimagecoordinates_flipaxisimgteamhttps://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/
qupath_roi_splitter0.1.0+galaxy1geojsonTo updateSplit ROI coordinates of QuPath TMA annotation by cell typeTo updatehttps://github.com/npinter/ROIsplitterImagingqupath_roi_splittergalaxyphhttps://github.com/npinter/ROIsplitter
spyboat0.1.2spyboatTo updateWavelet analysis for 3d-image stacksTo updatehttp://github.com/tensionhead/spyboatImaging, Graphicsspyboatiuchttps://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat
+ +
\ No newline at end of file diff --git a/results/imaging/tools.tsv b/results/imaging/tools.tsv new file mode 100644 index 00000000..45be5b1d --- /dev/null +++ b/results/imaging/tools.tsv @@ -0,0 +1,4 @@ +Galaxy wrapper id https://usegalaxy.eu usage https://usegalaxy.eu usage Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu Reviewed To keep +imagecoordinates_flipaxis 7 7 imagecoordinates_flipaxis Flip coordinate axes galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging imagecoordinates_flipaxis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ 0.1-2 pandas (0/1) (0/1) (1/1) False +qupath_roi_splitter 5 5 qupath_roi_splitter 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 0.1.0+galaxy1 geojson (0/1) (0/1) (1/1) False +spyboat 1 1 spyboat 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 0.1.2 spyboat (0/1) (0/1) (1/1) False diff --git a/results/imaging/tools_wordcloud.png b/results/imaging/tools_wordcloud.png new file mode 100644 index 00000000..56278830 Binary files /dev/null and b/results/imaging/tools_wordcloud.png differ diff --git a/results/microgalaxy/index.html b/results/microgalaxy/index.html new file mode 100644 index 00000000..08d81f6d --- /dev/null +++ b/results/microgalaxy/index.html @@ -0,0 +1,2423 @@ + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ExpandGalaxy wrapper idGalaxy wrapper versionConda versionConda idStatusbio.tool idbio.tool nameEDAM operationEDAM topicDescriptionbio.tool descriptionStatusSourceToolShed categoriesToolShed idGalaxy wrapper ownerGalaxy wrapper source
abricate1.0.11.0.1abricateUp-to-dateABRicateABRicateAntimicrobial resistance predictionGenomics, MicrobiologyMass screening of contigs for antiobiotic resistance genesMass screening of contigs for antimicrobial resistance or virulence genes.Up-to-datehttps://github.com/tseemann/abricateSequence Analysisabricateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/
aldex21.26.01.34.0bioconductor-aldex2To updatealdex2ALDEx2Statistical inferenceGene expression, Statistics and probabilityPerforms analysis Of differential abundance taking sample variation into accountA 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 updatehttps://github.com/ggloor/ALDEx_biocMetagenomicsaldex2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2
amplican1.14.01.24.0bioconductor-amplicanTo updateamplicanamplicanAlignment, Standardisation and normalisationPCR experiment, Statistics and probabilityAmpliCan 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 updatehttps://github.com/valenlab/amplicanSequence Analysisamplicaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican
ancombc1.4.02.4.0bioconductor-ancombcTo updateancombcANCOMBCDNA barcodingMicrobial ecology, MetagenomicsPerforms 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 updatehttps://github.com/FrederickHuangLin/ANCOMBCMetagenomicsancombciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc
antismash6.1.16.1.1antismashUp-to-dateantismashantiSMASHSequence clustering, Gene prediction, Differential gene expression analysisMolecular interactions, pathways and networks, Gene and protein familiesAntismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clustersRapid 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.Up-to-datehttps://antismash.secondarymetabolites.orgSequence Analysisantismashbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash
bakta1.8.21.9.1baktaTo updateBaktaBaktaGenome annotationGenomics, 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 & plasmidsTo updatehttps://github.com/oschwengers/baktaSequence Analysisbaktaiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta
bamtools2.5.22.5.2bamtoolsUp-to-dateOperate on and transform BAM datasets in various ways using bamtoolsUp-to-datehttps://github.com/pezmaster31/bamtoolsSequence Analysis, SAMbamtoolsdevteamhttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools
blast2go0.0.11b2g4pipeTo updateMaps BLAST results to GO annotation termsTo updatehttps://github.com/peterjc/galaxy_blast/tree/master/tools/blast2goOntology Manipulation, Sequence Analysisblast2gopeterjchttps://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go
blastxml_to_top_descr0.1.2pythonTo updateMake table of top BLAST match descriptionsTo updatehttps://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descrConvert Formats, Sequence Analysis, Text Manipulationblastxml_to_top_descrpeterjchttps://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr
busco5.5.05.6.1buscoTo updatebuscoBUSCOSequence assembly validation, Scaffolding, Genome assembly, Transcriptome assemblySequence assembly, Genomics, Transcriptomics, Sequence analysisBUSCO assess genome and annotation completenessProvides 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 updatehttps://gitlab.com/ezlab/busco/-/releasesSequence Analysisbuscoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/
cemitool1.18.11.26.0bioconductor-cemitoolTo updatecemitoolCEMiToolEnrichment analysis, Pathway or network analysisGene expression, Transcriptomics, Microarray experimentGene co-expression network analysis toolIt 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 updatehttps://www.bioconductor.org/packages/release/bioc/html/CEMiTool.htmlTranscriptomics, RNA, Statisticscemitooliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool
clustalw2.12.1clustalwUp-to-date\n clustal2\nClustalW multiple sequence alignment program for DNA or proteinsUp-to-datehttp://www.clustal.org/clustal2/Phylogenetics, Sequence Analysisclustalwdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw
codeml4.94.10.7pamlTo updateDetects positive selectionTo updatehttp://abacus.gene.ucl.ac.uk/software/paml.htmlPhylogeneticscodemliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml
combine_metaphlan_humann0.3.0pythonTo updatecombine_metaphlan_and_humannCombine Metaphlan and HUMAnNAggregationMetagenomics, Molecular interactions, pathways and networksCombine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances"This tool combine MetaPhlAn outputs and HUMANnN outputs." - Galaxy tool wrapperTo updateMetagenomicscombine_metaphlan2_humann2bebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2
compare_humann2_output0.2.0To updatecompare_humann2_outputsCompare HUMAnN2 outputsComparisonMetagenomics, Gene and protein familiesCompare 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 wrapperTo updateMetagenomicscompare_humann2_outputbebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output
concoct1.1.01.1.0concoctUp-to-dateconcoctCONCOCTSequence clustering, Read binningMetagenomicsCONCOCT (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-datehttps://github.com/BinPro/CONCOCTMetagenomicsconcoctiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct
cutadapt4.64.6cutadaptUp-to-datecutadaptCutadaptSequence trimmingGenomics, Probes and primers, SequencingFlexible 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-datehttps://cutadapt.readthedocs.org/en/stable/Fasta Manipulation, Fastq Manipulation, Sequence Analysiscutadaptlparsonshttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt
das_tool1.1.61.1.7das_toolTo updatedastooldastoolRead binningMetagenomicsDAS Tool for genome resolved metagenomicsDAS 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.To updatehttps://github.com/cmks/DAS_ToolMetagenomicsdas_tooliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool
disco1.2discoTo updatediscoDISCOProtein sequence analysisStructure determinationDISCO is a overlap-layout-consensus (OLC) metagenome assemblerDISCO 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 updatehttp://disco.omicsbio.org/Metagenomics, Assemblydiscoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/
ectyper1.0.01.0.0ectyperUp-to-dateEC-Typer - in silico serotyping of Escherichia coli speciesUp-to-datehttps://github.com/phac-nml/ecoli_serotypingSequence Analysisectypernmlhttps://github.com/phac-nml/ecoli_serotyping
eggnog_mapper2.1.82.1.12eggnog-mapperTo updateeggnog-mapper-v2eggNOG-mapper v2Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrievalMetagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysiseggnog-mapper fast functional annotation of novel sequencesEggNOG-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 updateProteomicseggnog_mappergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper
export2graphlan0.200.22export2graphlanTo updateexport2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAnTo updatehttps://bitbucket.org/CibioCM/export2graphlan/overviewMetagenomicsexport2graphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/
fargene0.10.1fargeneUp-to-datefARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )Up-to-datehttps://github.com/fannyhb/fargeneSequence Analysisfargeneiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene
fastp0.23.4fastpTo update\n fastp\nFast all-in-one preprocessing for FASTQ filesTo updatehttps://github.com/OpenGene/fastpSequence Analysisfastpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp
fastqe0.3.1+galaxy00.3.1fastqeTo updateFASTQETo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqeSequence Analysisfastqeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe
fasttree2.1.102.1.11fasttreeTo updatefasttreeFastTreePhylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)Phylogenetics, Sequence analysisFastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVLInfers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.To updatehttp://www.microbesonline.org/fasttree/Phylogeneticsfasttreeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree
filtlong0.2.10.2.1filtlongUp-to-date\n filtlong\nFiltlong - Filtering long reads by qualityUp-to-datehttps://github.com/rrwick/FiltlongFastq Manipulation, Sequence Analysisfiltlongiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong
flye2.9.12.9.3flyeTo updateAssembly of long and error-prone reads.To updatehttps://github.com/fenderglass/Flye/Assemblyflyebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/flye
format_metaphlan2_output0.2.0To updateformat_metaphlan2_outputFormat metaphlan2 outputFormattingTaxonomy, MetagenomicsFormat 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 wrapperTo updateMetagenomicsformat_metaphlan2_outputbebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/
fraggenescan1.31fraggenescanTo updatefraggenescanFragGeneScanGene predictionGenetics, Sequence analysisTool for finding (fragmented) genes in short readApplication for finding (fragmented) genes in short readsTo updatehttps://sourceforge.net/projects/fraggenescan/Sequence Analysisfraggenescaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/
goenrichment2.0.12.0.1goenrichmentUp-to-dategoenrichmentGOEnrichmentGene-set enrichment analysisTranscriptomicsPerforms 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-datehttps://github.com/DanFaria/GOEnrichmentGenome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment
goseq1.50.01.54.0bioconductor-goseqTo updategoseqGOseqGene functional annotationRNA-Seqgoseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq dataDetect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.To updatehttps://bioconductor.org/packages/release/bioc/html/goseq.htmlStatistics, RNA, Micro-array Analysisgoseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq
graphlan1.1.3graphlanTo updateGraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic treesTo updatehttps://bitbucket.org/nsegata/graphlan/overviewMetagenomics, Graphics, Phylogeneticsgraphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/
gubbins3.2.13.3.1gubbinsTo updategubbinsGubbinsGenotyping, Phylogenetic inference, Ancestral reconstructionPhylogeny, Genotype and phenotype, Whole genome sequencingGubbins - bacterial recombination detectionGubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.To updateSequence Analysisgubbinsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins
hifiasm_meta0.3.1hamtv0.3.1hifiasm_metaTo updateA hifiasm fork for metagenome assembly using Hifi reads.To updatehttps://github.com/xfengnefx/hifiasm-metaMetagenomicshifiasm_metagalaxy-australiahttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta
humann3.83.8humannUp-to-datehumannhumannSpecies frequency estimation, Taxonomic classification, Phylogenetic analysisMetagenomics, PhylogenomicsHUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolutionHUMAnN 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-datehttp://huttenhower.sph.harvard.edu/humannMetagenomicshumanniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/humann
hypo1.0.31.0.3hypoUp-to-dateHyPoHyPoOptimisation and refinement, Genome assemblySequence assembly, GenomicsSuper Fast & Accurate Polisher for Long Read Genome AssembliesHyPo, 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-datehttps://github.com/kensung-lab/hypoAssemblyhypoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo
idba_ud1.1.3idbaTo updateidbaIDBASequence assemblySequence assemblyWrappers 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 updatehttps://i.cs.hku.hk/~alse/hkubrg/projects/index.htmlAssemblyidbaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud
interproscan5.59-91.05.59_91.0interproscanTo updateinterproscan_ebiInterProScan (EBI)Sequence motif recognition, Protein feature detectionGene and protein families, Sequence analysisInterproscan queries the interpro database and provides annotations.Scan sequences against the InterPro protein signature databases.To updatehttp://www.ebi.ac.uk/Tools/pfa/iprscan5/Sequence Analysisinterproscanbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan
iqtree2.1.22.2.6iqtreeTo updateEfficient phylogenomic software by maximum likelihoodTo updatehttp://www.iqtree.org/Phylogeneticsiqtreeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/
itsx1.1.31.1.3itsxUp-to-dateITSxITSxSequence feature detectionFunctional, regulatory and non-coding RNA, MicrobiologyITSx 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-datehttps://microbiology.se/software/itsx/Metagenomicsitsxbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/itsx
jbrowse1.16.111.16.11jbrowseUp-to-datejbrowseJBrowseGenome visualisationGenomicsJBrowse Genome Browser integrated as a Galaxy ToolSlick, 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-datehttps://jbrowse.orgSequence Analysisjbrowseiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse
jellyfish2.3.0kmer-jellyfishTo updateJellyfishJellyfishk-mer countingSequence analysis, GenomicsJellyfish is a tool for fast, memory-efficient counting of k-mers in DNAA command-line algorithm for counting k-mers in DNA sequence.To updatehttps://github.com/gmarcais/JellyfishAssemblyjellyfishiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish
kc-align1.0.21.0.2kcalignUp-to-datekc-alignkc-alignMultiple sequence alignmentMappingKc-Align custom toolA fast and accurate tool for performing codon-aware multiple sequence alignmentsUp-to-datehttps://github.com/davebx/kc-alignSequence Analysiskc_aligniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align
kleborate2.3.22.3.2kleborateUp-to-datekleborateKleborateMultilocus sequence typing, Genome assembly, Virulence predictionPublic health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencingScreen 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-datehttps://github.com/katholt/Kleborate/wikiMetagenomicskleborateiuchttps://github.com/katholt/Kleborate
kofamscan1.3.01.3.0kofamscanUp-to-dateGene function annotation tool based on KEGG Orthology and hidden Markov modelUp-to-datehttps://github.com/takaram/kofam_scanSequence Analysiskofamscaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan
kraken1.1.1krakenTo updateKraken 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 updatehttp://ccb.jhu.edu/software/kraken/Metagenomicskrakendevteamhttps://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/
kraken22.1.12.1.3kraken2To updateKraken2 for taxonomic designation.To updatehttp://ccb.jhu.edu/software/kraken/Metagenomicskraken2iuchttps://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/
kraken_biom1.2.01.2.0kraken-biomUp-to-dateCreate BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)Up-to-datehttps://github.com/smdabdoub/kraken-biomMetagenomicskraken_biomiuchttps://github.com/smdabdoub/kraken-biom
kraken_taxonomy_report0.0.31.70biopythonTo updateKraken taxonomy reportTo updatehttps://github.com/blankenberg/Kraken-Taxonomy-ReportMetagenomicskraken_taxonomy_reportiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report
legsta0.5.10.5.1legstaUp-to-datePerforms in silico Legionella pneumophila sequence based typing.Up-to-datehttps://github.com/tseemann/legstaSequence Analysislegstaiuchttps://github.com/tseemann/legsta
lighter1.01.1.2lighterTo updateLighter is a kmer-based error correction method for whole genome sequencing dataTo updateSequence Analysis, Fasta Manipulationlighterbgrueninghttps://github.com/mourisl/Lighter
lineagespot1.4.0r-baseTo updatelineagespotlineagespotVariant callingMetagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variationIdentification 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 updatehttps://www.bioconductor.org/packages/release/bioc/html/lineagespot.htmlMetagenomics, Sequence Analysislineagespotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot
lotus22.302.32lotus2To updatelotus2lotus2Sequence feature detectionMetagenomicsLotuS2 OTU processing pipelineLotuS2 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.To updatehttp://lotus2.earlham.ac.uk/Metagenomicslotus2earlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2
maaslin20.99.120.99.12maaslin2Up-to-dateMaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.Up-to-datehttp://huttenhower.sph.harvard.edu/maaslinMetagenomicsmaaslin2iuchttps://github.com/biobakery/Maaslin2
maker2.31.113.01.03makerTo updatemakerMAKERGenome annotationGenomics, DNA, Sequence analysisMAKER 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 updatehttp://www.yandell-lab.org/software/maker.htmlSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/maker
mapseq2.1.1perlTo updatefast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.To updatehttps://github.com/jfmrod/MAPseqMetagenomicsmapseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq
maxbin22.2.7maxbin2To updatemaxbinMaxBinSequence assemblyMetagenomics, Sequence assembly, Microbiologyclusters metagenomic contigs into binsSoftware for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.To updatehttps://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.htmlMetagenomicsmaxbin2mbernthttps://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/
mcl14.13722.282mclTo updateMarkov Cluster AlgorithmTo updatehttp://micans.org/mcl/Sequence Analysis, Metagenomicsmclbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/mcl
mcl22.28222.282mclUp-to-datemclMCLClustering, Network analysis, Gene regulatory network analysisMolecular interactions, pathways and networksThe Markov Cluster Algorithm, a cluster algorithm for graphsMCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.Up-to-datehttps://micans.org/mcl/man/mcl.htmlSequence Analysismcliuchttps://github.com/galaxyproject/tools-iuc/tree/master/mcl
megahit1.2.91.2.9megahitUp-to-datemegahitMEGAHITGenome assemblyMetagenomics, Sequencing, Ecology, Sequence assemblyAn 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-datehttps://github.com/voutcn/megahitSequence Analysis, Assembly, Metagenomicsmegahitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit
megahit_contig2fastg1.1.31.2.9megahitTo updatemegahitMEGAHITGenome assemblyMetagenomics, Sequencing, Ecology, Sequence assemblyA 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 updatehttps://github.com/voutcn/megahit/blob/master/tools/toolkit.cppSequence Analysis, Assembly, Metagenomicsmegahit_contig2fastgiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg
merqury1.31.3merquryUp-to-datemerquryMerquryGenome assembly, k-mer counting, Scaffolding, Phasing, De-novo assemblySequence assembly, Whole genome sequencing, Plant biologyMerqury 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-datehttps://github.com/marbl/merquryAssemblymerquryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury
meryl1.31.3merquryUp-to-datemerylMerylk-mer countingWhole genome sequencing, Genomics, Sequence analysis, SequencingMeryl 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-datehttps://github.com/marbl/merylAssemblymeryliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl
metabat22.152.15metabat2Up-to-dateMetaBAT_2MetaBAT 2Read binning, Sequence assembly, Genome annotationMetagenomics, Sequence assembly, Metagenomic sequencingMetaBAT2 (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 binningUp-to-datehttps://bitbucket.org/berkeleylab/metabat/src/master/Metagenomicsmetabat2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/
metagene_annotator1.0.01.0metagene_annotatorTo updateMetaGeneAnnotator gene-finding program for prokaryote and phageTo updateSequence Analysismetagene_annotatorgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator
metaphlan4.0.64.0.6metaphlanUp-to-datemetaphlanMetaPhlAnNucleic acid sequence analysis, Phylogenetic tree analysisMetagenomics, PhylogenomicsMetaPhlAn for Metagenomic Phylogenetic AnalysisComputational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.Up-to-datehttps://github.com/biobakery/MetaPhlAnMetagenomicsmetaphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/
minia3.2.63.2.6miniaUp-to-dateminiaMiniaGenome assemblySequence assemblyShort-read assembler based on a de Bruijn graphShort-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.Up-to-datehttps://gatb.inria.fr/software/minia/Assemblyminiaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/minia
miniasm0.3_r1790.3miniasmTo updateMiniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)To updatehttps://github.com/lh3/miniasmAssemblyminiasmiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm
minipolish0.1.30.1.3minipolishUp-to-dateminipolishminipolishLocalised reassembly, Read depth analysisSequence assembly, SequencingPolishing miniasm assembliesA 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-datehttps://github.com/rrwick/MinipolishSequence Analysisminipolishbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/minipolish
miniprot0.120.12miniprotUp-to-dateAlign a protein sequence against a genome with affine gap penalty, splicing and frameshift.Up-to-datehttps://github.com/lh3/miniprotSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot
mitos1.1.42.1.6mitosTo updatemitosMITOSGenome annotationZoology, Whole genome sequencingde-novo annotation of metazoan mitochondrial genomesDe novo metazoan mitochondrial genome annotation.To updatehttp://mitos.bioinf.uni-leipzig.de/Sequence Analysismitosiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos
mlst2.22.02.23.0mlstTo updatemlstMLSTTaxonomic classificationImmunoproteins, genes and antigensScan contig files against PubMLST typing schemesMulti Locus Sequence Typing from an assembled genome or from a set of reads.To updatehttps://github.com/tseemann/mlstSequence Analysismlstiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst
multigsea1.8.01.12.0bioconductor-multigseaTo updatemultiGSEAmultiGSEAGene-set enrichment analysis, Aggregation, Pathway analysisMetabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small moleculesGSEA-based pathway enrichment analysis for multi-omics dataA 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.To updatehttps://bioconductor.org/packages/devel/bioc/html/multiGSEA.htmlTranscriptomics, Proteomics, Statisticsmultigseaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea
multiqc1.111.19multiqcTo updatemultiqcMultiQCValidationSequencing, BioinformaticsMultiQC aggregates results from bioinformatics analyses across many samples into a single reportMultiQC 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 updatehttp://multiqc.info/Fastq Manipulation, Statistics, Visualizationmultiqciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc
nanoplot1.41.01.42.0nanoplotTo updatePlotting tool for long read sequencing data and alignmentsTo updatehttps://github.com/wdecoster/NanoPlotVisualizationnanoplotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/
nextclade2.7.02.14.0nextalignTo updateIdentify differences between your sequences and a reference sequence used by NextstrainTo updatehttps://github.com/nextstrain/nextcladeSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade
nextdenovo2.5.02.5.2nextdenovoTo updatenextdenovoNextDenovoDe-novo assembly, Genome assemblySequencing, Sequence assemblyString graph-based de novo assembler for long readsNextDenovo 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 updatehttps://github.com/Nextomics/NextDenovoAssemblynextdenovobgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo
nonpareil3.1.13.4.1nonpareilTo updateEstimate average coverage in metagenomic datasetsTo updatehttp://nonpareil.readthedocs.ioMetagenomicsnonpareiliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil
obisindicators0.0.2r-baseTo updateCompute biodiveristy indicators for marine data from obisTo updatehttps://github.com/Marie59/obisindicatorsEcologyecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators
orfipy0.0.40.0.4orfipyUp-to-dateorfipyorfipyCoding region prediction, Database search, Transcriptome assembly, De-novo assemblyComputer science, RNA-Seq, Transcriptomics, Small moleculesGalaxy wrapper for ORFIPYA 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-datehttps://github.com/urmi-21/orfipySequence Analysisorfipyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy
pfamscan1.61.6pfam_scanUp-to-datepfamscanPfamScanProtein sequence analysisSequence analysisSearch 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-datehttp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/Sequence Analysispfamscanbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/pfamscan
pharokka1.3.2\n pharokka\nTo update\n pharokka\nrapid standardised annotation tool for bacteriophage genomes and metagenomesTo updatehttps://github.com/gbouras13/pharokkaGenome annotationpharokkaiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka
phyml3.3.202204083.3.20220408phymlUp-to-datephymlPhyMLPhylogenetic tree generation (maximum likelihood and Bayesian methods)Phylogenetics, Bioinformatics, PhylogeneticsPhyML is a phylogeny software based on the maximum-likelihood principle.Phylogenetic estimation software using Maximum LikelihoodUp-to-datehttp://www.atgc-montpellier.fr/phyml/Phylogeneticsphymliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml
plasmidfinder2.1.62.1.6plasmidfinderUp-to-datePlasmidFinderPlasmidFinderGenome assembly, Scaffolding, Multilocus sequence typingWhole 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-datehttps://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/Sequence Analysisplasmidfinderiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder
prokka1.14.61.14.6prokkaUp-to-dateprokkaProkkaGene prediction, Coding region prediction, Genome annotationGenomics, Model organisms, VirologyRapid annotation of prokaryotic genomesSoftware tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.Up-to-datehttp://github.com/tseemann/prokkaSequence Analysisprokkacrs4https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/
proteinortho6.2.36.3.1proteinorthoTo updateproteinorthoProteinorthoHomology-based gene predictionPhylogenyProteinortho is a tool to detect orthologous proteins/genes within different species.Proteinortho is a tool to detect orthologous genes within different speciesTo updatehttps://gitlab.com/paulklemm_PHD/proteinorthoProteomicsproteinorthoiuchttps://gitlab.com/paulklemm_PHD/proteinortho
pycoqc2.5.22.5.2pycoqcUp-to-dateQC metrics for ONT BasecallingUp-to-datehttps://github.com/tleonardi/pycoQCNanoporepycoqciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc
quast5.2.05.2.0quastUp-to-datequastQUASTVisualisation, Sequence assembly validationSequence assemblyQuast (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-datehttp://quast.bioinf.spbau.ru/Assemblyquastiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/quast
racon1.5.01.5.0raconUp-to-dateRaconRaconGenome assembly, Mapping assembly, Sequence trimmingWhole genome sequencing, Sequence assembly, Plant biologyConsensus 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 readsUp-to-datehttps://github.com/isovic/raconSequence Analysisraconbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/racon
raxml8.2.128.2.13raxmlTo updateraxmlRAxMLSequence analysis, Phylogenetic tree analysisPhylogenetics, Sequence analysisRAxML - A Maximum Likelihood based phylogenetic inferenceA tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.To updatehttp://www.exelixis-lab.org/web/software/raxml/Phylogeneticsraxmliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml
read_it_and_keep0.2.20.3.0read-it-and-keepTo updateRapid decontamination of SARS-CoV-2 sequencing readsTo updatehttps://github.com/GenomePathogenAnalysisService/read-it-and-keepSequence Analysisread_it_and_keepiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep
recentrifuge1.12.11.13.2recentrifugeTo updateRecentrifugeRecentrifugeTaxonomic classification, Expression analysis, Cross-assemblyMetagenomics, 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.To updatehttps://github.com/khyox/recentrifugeMetagenomicsrecentrifugeiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge
roary3.13.03.13.0roaryUp-to-dateroaryRoaryGenome assemblyDNA, Genomics, MappingRoary the pangenome pipelineA 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-datehttps://sanger-pathogens.github.io/Roary/Sequence Analysisroaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/roary
salmon1.10.11.10.2salmonTo updateSalmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.To updatehttps://github.com/COMBINE-lab/salmonSequence Analysis, RNA, Transcriptomicsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/salmon
sarscov2formatter1.01.0sarscov2formatterUp-to-datesarscov2formatter custom scriptUp-to-datehttps://github.com/nickeener/sarscov2formatterSequence Analysissarscov2formatteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter
sarscov2summary0.10.5sarscov2summaryTo updatesarscov2summary custom scriptTo updatehttps://github.com/nickeener/sarscov2summarySequence Analysissarscov2summaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary
scoary1.6.161.6.16scoaryUp-to-dateScoary calculates the assocations between all genes in the accessory genome and the traits.Up-to-datehttps://github.com/AdmiralenOla/ScoaryMetagenomicsscoaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary
semibin2.0.22.0.2semibinUp-to-datesemibinSemiBinSequence assembly, Read binningMetagenomics, Machine learning, Microbial ecology, Sequence assemblySemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural NetworksCommand tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.Up-to-datehttps://semibin.readthedocs.io/en/latest/Metagenomicssemibiniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin
shovill1.1.01.1.0shovillUp-to-dateshovillshovillGenome assemblyGenomics, Microbiology, Sequence assemblyFaster de novo assembly pipeline based around SpadesShovill 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-datehttps://github.com/tseemann/shovillAssemblyshovilliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill
sistr_cmd1.1.11.1.1sistr_cmdUp-to-dateSISTR in silico serotyping toolUp-to-datehttps://github.com/phac-nml/sistr_cmdSequence Analysissistr_cmdnml
snippy4.6.0snippyTo updatesnippysnippyPhylogenetic tree visualisation, Phylogenetic tree generation, Variant callingGenomics, Model organisms, DNA polymorphism, PhylogeneticsContains the snippy tool for characterising microbial snpsRapid haploid variant calling and core SNP phylogeny generation.To updatehttps://github.com/tseemann/snippySequence Analysissnippyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy
sonneityping2021020120210201sonneitypingUp-to-dateScripts for parsing Mykrobe predict results for Shigella sonnei.Up-to-datehttps://github.com/katholt/sonneitypingSequence Analysissonneitypingiuchttps://github.com/katholt/sonneityping
spades3.15.53.15.5spadesUp-to-dateSPAdes 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.Up-to-datehttps://github.com/ablab/spadesAssembly, RNA, Metagenomicsspadesiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/spades
spotyping2.12.1spotypingUp-to-datespotypingSpoTypingVariant pattern analysisMicrobiology, Sequencing, Sequence composition, complexity and repeats, Genetic variationSpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence readsFast and accurate in silico Mycobacterium spoligotyping from sequence reads.Up-to-datehttps://github.com/xiaeryu/SpoTyping-v2.0Sequence Analysisspotypingiuchttps://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine
srst20.3.70.2.0srst2To updateShort Read Sequence Typing for Bacterial PathogensTo updateSequence Analysissrst2nml
srst20.2.01.19samtoolsTo updateSRST2 Short Read Sequence Typing for Bacterial PathogensTo updatehttp://katholt.github.io/srst2/Metagenomicssrst2iuchttps://github.com/katholt/srst2
structure2.3.42.3.4structureUp-to-datestructureStructureGenetic variation analysisPopulation geneticsfor 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-datePhylogenetics, Variant Analysisstructureiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/structure
t2t_report1.0.00.9.0taxonomyTo updateSummarize taxonomyTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicst2t_reportdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report
taxonomy_krona_chart2.7.1+galaxy02.8.1kronaTo updatekronaKronaVisualisationMetagenomicsKrona pie chart from taxonomic profileKrona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).To updatehttp://sourceforge.net/projects/krona/Assemblytaxonomy_krona_chartcrs4https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart
transtermhp2.09transtermhpTo updateFinds rho-independent transcription terminators in bacterial genomesTo updateSequence Analysistranstermhpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp
trim_galore0.6.70.6.10trim-galoreTo updatetrim_galoreTrim GaloreSequence trimmingSequence analysisTrim Galore adaptive quality and adapter trimmerA 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 updatehttp://www.bioinformatics.babraham.ac.uk/projects/trim_galore/Sequence Analysis, Fastq Manipulationtrim_galorebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/trim_galore
unicycler0.5.00.5.0unicyclerUp-to-dateunicyclerUnicyclerGenome assembly, AggregationMicrobiology, Genomics, Sequencing, Sequence assemblyUnicycler 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-datehttps://github.com/rrwick/UnicyclerAssemblyunicycleriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler
usher0.2.10.6.3usherTo updateUShER toolkit wrappersTo updatehttps://github.com/yatisht/usherPhylogeneticsusheriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/usher
valet1.0valetTo updateA pipeline for detecting mis-assemblies in metagenomic assemblies.To updatehttps://github.com/marbl/VALETMetagenomicsvaletiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/valet
vapor1.0.21.0.2vaporUp-to-datevaporVAPORData retrieval, De-novo assembly, Read mappingWhole genome sequencing, Mapping, Sequence assemblyClassify Influenza samples from raw short read sequence dataVAPOR 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-datehttps://github.com/connor-lab/vaporSequence Analysisvaporiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor
wtdbg2.52.5wtdbgUp-to-datewtdbg2wtdbg2Genome assembly, De-novo assemblySequence assembly, SequencingWTDBG 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-datehttps://github.com/ruanjue/wtdbg2Assemblywtdbgbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/wtdbg
+ +
\ No newline at end of file diff --git a/results/microgalaxy/tools.tsv b/results/microgalaxy/tools.tsv new file mode 100644 index 00000000..2c7ebc14 --- /dev/null +++ b/results/microgalaxy/tools.tsv @@ -0,0 +1,336 @@ +Galaxy wrapper id https://usegalaxy.eu usage https://usegalaxy.eu usage Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu Reviewed To keep +abricate 1257 1257 abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ 1.0.1 abricate 1.0.1 (3/3) (3/3) (3/3) True True +adapter_removal 37 37 adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval AdapterRemoval 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. Sequence trimming, Sequence merging, Primer removal 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/ 2.3.3 adapterremoval 2.3.3 (0/1) (0/1) (1/1) True False +aldex2 13 13 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) True True +align_back_trans 11 11 align_back_trans 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 0.0.10 biopython 1.70 (0/1) (0/1) (1/1) True False +amplican 12 12 amplican AmpliCan is an analysis tool for genome editing. amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 (0/1) (0/1) (1/1) True True +ancombc 4 4 ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 (0/1) (0/1) (1/1) True True +annotatemyids 1175 1175 annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids 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. Annotation To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids 3.17.0 bioconductor-org.hs.eg.db 3.18.0 (1/1) (1/1) (1/1) True False +antarna 2 2 antarna 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/ 1.1 antarna 2.0.1.2 (0/1) (0/1) (1/1) True False +antismash 279 279 antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Up-to-date https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash 6.1.1 antismash 6.1.1 (1/1) (1/1) (1/1) True True +arriba 28 28 arriba, arriba_draw_fusions, arriba_get_filters 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 2.4.0 arriba 2.4.0 (0/3) (3/3) (3/3) True False +augustus 516 516 augustus 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 3.1.0 augustus 3.5.0 (1/1) (1/1) (1/1) True False +augustus 516 516 augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus AUGUSTUS 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. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus 3.4.0 augustus 3.5.0 (2/2) (2/2) (2/2) True False +bakta 151 151 bakta """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.""" Bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis To update https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta 1.8.2 bakta 1.9.1 (0/1) (1/1) (1/1) True True +bamhash 15 15 bamhash 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 1.1 bamhash 1.1 (0/1) (0/1) (1/1) True False +bamtools 208 208 bamtools 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 2.5.2 bamtools 2.5.2 (1/1) (0/1) (1/1) True True +bamtools_split 46 46 bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag 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 2.5.2 bamtools 2.5.2 (4/4) (0/4) (4/4) True False +barrnap 160 160 barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap Barrnap 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). Gene prediction Genomics, Model organisms, Model organisms To update Sequence Analysis barrnap iuc 1.2.2 barrnap 0.9 (0/1) (1/1) (1/1) True False +bax2bam 8 8 bax2bam 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 0.0.11 bax2bam 0.0.11 (1/1) (0/1) (1/1) True False +bed_to_protein_map 49 49 bed_to_protein_map 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 0.2.0 python (1/1) (1/1) (1/1) True False +bellerophon 123 123 bellerophon 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 1.0 bellerophon 1.0 (1/1) (1/1) (1/1) True False +biscot 1 1 biscot 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 2.3.3 biscot 2.3.3 (0/1) (0/1) (1/1) True False +blast2go 101 101 blast2go 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 0.0.11 b2g4pipe (0/1) (0/1) (0/1) False +blast_parser 27 27 blast_parser 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 0.1.2 (0/1) (0/1) (1/1) True False +blastxml_to_gapped_gff3 24 24 blastxml_to_gapped_gff3 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 1.1 bcbiogff 0.6.6 (1/1) (1/1) (1/1) True False +blastxml_to_top_descr 159 159 blastxml_to_top_descr 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 0.1.2 python (0/1) (0/1) (1/1) False +blobtoolkit 21 21 blobtoolkit 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 4.0.7 (0/1) (1/1) (1/1) True False +blockbuster 34 34 blockbuster 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 0.1.2 blockbuster 0.0.1.1 (1/1) (1/1) (1/1) True False +blockclust 15 15 blockclust 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 1.1.1 blockclust 1.1.1 (1/1) (1/1) (1/1) True False +braker 17 17 braker 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 2.1.6 (0/1) (0/1) (1/1) True False +braker3 10 10 braker3 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 3.0.6 (0/1) (1/1) (1/1) True False +busco 1804 1804 busco BUSCO assess genome and annotation completeness busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ 5.5.0 busco 5.6.1 (1/1) (1/1) (1/1) True True +bwameth 201 201 bwameth 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 0.2.6 bwameth 0.2.7 (1/1) (1/1) (1/1) True False +cap3 101 101 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 (0/1) (1/1) (1/1) True False +cemitool 9 9 cemitool Gene co-expression network analysis tool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment 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 1.18.1 bioconductor-cemitool 1.26.0 (1/1) (0/1) (1/1) True True +charts 287 287 charts Enables advanced visualization options in Galaxy Charts To update Visualization charts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ 1.0.1 r-getopt (0/1) (0/1) (0/1) True False +chipseeker 418 418 chipseeker 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 1.32.0 bioconductor-chipseeker 1.38.0 (1/1) (1/1) (1/1) True False +chromeister 182 182 chromeister 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 1.5.a chromeister 1.5.a (0/1) (1/1) (1/1) True False +circexplorer 8 8 circexplorer 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 1.1.9.0 circexplorer 1.1.10 (0/1) (1/1) (1/1) True False +circexplorer2 16 16 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 (0/1) (0/1) (1/1) True False +clair3 68 68 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 0.1.12 clair3 1.0.5 (0/1) (0/1) (1/1) True False +clustalw 651 651 clustalw ClustalW multiple sequence alignment program for DNA or proteins " + clustal2 + " Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) True True +cmsearch_deoverlap 1 1 cmsearch_deoverlap 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 0.08+galaxy0 perl (0/1) (0/1) (1/1) True False +cmv 1 1 cmcv, cmv, hmmcv, hmmv 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 1.0.8 cmv 1.0.8 (0/4) (0/4) (2/4) True False +codeml 29 29 codeml Detects positive selection To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) True True +cofold 8 8 cofold 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 2.0.4.0 cofold 2.0.4 (0/1) (0/1) (1/1) True False +combine_metaphlan_humann 9 9 combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann Combine Metaphlan and HUMAnN """This tool combine MetaPhlAn outputs and HUMANnN outputs."" - Galaxy tool wrapper" Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 0.3.0 python (0/1) (0/1) (1/1) True True +compare_humann2_output 10 10 compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs Compare HUMAnN2 outputs """This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples."" - Galaxy tool wrapper" Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 (0/1) (0/1) (0/1) True True +compute_motif_frequencies_for_all_motifs 2 2 compute_motif_frequencies_for_all_motifs 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 1.0.0 (0/1) (1/1) (1/1) True False +concoct 29 29 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering 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. concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) True True +count_gff_features 49 49 count_gff_features Count GFF Features To update Sequence Analysis count_gff_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features 0.2 galaxy-ops 1.1.0 (1/1) (1/1) (1/1) True False +crispr_studio 30 30 crispr_studio 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/ 1+galaxy0 crispr_studio 1 (0/1) (0/1) (1/1) True False +crosscontamination_barcode_filter 17 17 crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 (1/1) (0/1) (1/1) True False +custom_pro_db 57 57 custom_pro_db 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 1.22.0 bioconductor-rgalaxy 1.37.1 (1/1) (1/1) (1/1) True False +cutadapt 5090 5090 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming Genomics, Probes and primers, Sequencing 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 4.6 cutadapt 4.6 (1/1) (1/1) (1/1) True True +das_tool 17 17 Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics To update https://github.com/cmks/DAS_Tool Metagenomics das_tool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool 1.1.6 das_tool 1.1.7 (0/2) (0/2) (2/2) True True +dbbuilder 161 161 dbbuilder 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 0.3.4 wget (0/1) (1/1) (1/1) True False +decoyfasta 15 15 Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta (0/1) (0/1) (0/1) True False +delete_overlapping_indels 2 2 delete_overlapping_indels 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 1.0.0 (0/1) (0/1) (1/1) True False +deseq2 4990 4990 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis Transcriptomics 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 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) True False +dewseq 11 11 dewseq 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 0.1.0+galaxy0 python (0/1) (0/1) (1/1) True False +dexseq 75 75 dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq DEXSeq 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. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 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 1.44 bioconductor-dexseq 1.48.0 (3/3) (3/3) (3/3) True False +dialignr 1 1 dialignr 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 1.2.0 bioconductor-dialignr 2.10.0 (0/1) (0/1) (1/1) True False +diann 3 3 diann 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 1.8.1 (0/1) (1/1) (1/1) True False +diapysef 11 11 diapysef 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 0.3.5.0 diapysef 1.0.10 (0/1) (1/1) (1/1) True False +diffacto 5 5 diffacto 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 1.0.6 diffacto 1.0.6 (0/1) (0/1) (1/1) True False +disco 42 42 disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ disco 1.2 (1/1) (0/1) (1/1) True True +dotknot 1 1 dotknot 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 1.3.1 vienna_rna (0/1) (0/1) (1/1) True False +dropletutils 126 126 dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils DropletUtils 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. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics 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/ 1.10.0 bioconductor-dropletutils 1.22.0 (1/1) (1/1) (1/1) True False +dropletutils 126 126 dropletutils_empty_drops, dropletutils_read_10x 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/ 1.0.4 dropletutils-scripts 0.0.5 (2/2) (0/2) (2/2) True False +ectyper 53 53 ectyper 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 1.0.0 ectyper 1.0.0 (0/1) (0/1) (1/1) True True +edger 945 945 edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edgeR 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. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 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 3.36.0 bioconductor-edger 4.0.2 (1/1) (1/1) (1/1) True False +eggnog_mapper 498 498 eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 (1/3) (3/3) (3/3) True True +egsea 177 177 egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology 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 1.20.0 bioconductor-egsea 1.28.0 (1/1) (1/1) (1/1) True False +exomedepth 29 29 exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth ExomeDepth 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. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases 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 1.1.0 r-exomedepth 1.1.16 (1/1) (0/1) (1/1) True False +exonerate 59 59 exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks 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 2.4.0 exonerate 2.4.0 (1/1) (1/1) (1/1) True False +export2graphlan 200 200 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ 0.20 export2graphlan 0.22 (1/1) (1/1) (1/1) True True +express 12 12 express 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 1.1.1 eXpress 1.5.1 (0/1) (1/1) (1/1) True False +fargene 52 52 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene 0.1 fargene 0.1 (1/1) (0/1) (1/1) True True +fasta_nucleotide_color_plot 15 15 fasta_nucleotide_color_plot 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 1.0.1 openjdk (1/1) (0/1) (1/1) True False +fastani 250 250 fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani iuc 1.3 fastani 1.34 (0/1) (0/1) (1/1) True False +fastp 2803 2803 fastp Fast all-in-one preprocessing for FASTQ files " + fastp + " To update https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp fastp 0.23.4 (1/1) (1/1) (1/1) True True +fastqe 1266 1266 fastqe FASTQE To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) True True +fasttree 379 379 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree 2.1.10 fasttree 2.1.11 (1/1) (1/1) (1/1) True True +feature_alignment 1 1 feature_alignment 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 0.11.0 msproteomicstools 0.11.0 (0/1) (0/1) (1/1) True False +featurecounts 4679 4679 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation Sequencing To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) True False +feelnc 46 46 feelnc Galaxy wrapper for FEELnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc 0.2.1 feelnc 0.2 (1/1) (0/1) (1/1) True False +fgsea 307 307 fgsea Perform gene set testing using fgsea fgsea 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. Gene-set enrichment analysis Genetics 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 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 (1/1) (1/1) (1/1) True False +filter_by_fasta_ids 426 426 filter_by_fasta_ids 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 2.3 python (1/1) (1/1) (1/1) True False +filtlong 617 617 filtlong Filtlong - Filtering long reads by quality " + filtlong + " Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong 0.2.1 filtlong 0.2.1 (1/1) (1/1) (1/1) True True +find_diag_hits 5 5 find_diag_hits 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 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) True False +flash 74 74 flash Fast Length Adjustment of SHort reads flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash 1.2.11 flash 1.2.11 (1/1) (0/1) (1/1) True False +flashlfq 17 17 flashlfq 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 1.0.3.1 flashlfq 1.2.6 (0/1) (1/1) (1/1) True False +flye 1499 1499 flye Assembly of long and error-prone reads. To update https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.1 flye 2.9.3 (1/1) (1/1) (1/1) True True +format_metaphlan2_output 166 166 format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output Format metaphlan2 output """This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains)."" - Galaxy tool wrapper" Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ 0.2.0 (0/1) (0/1) (1/1) True True +fraggenescan 68 68 fraggenescan Tool for finding (fragmented) genes in short read fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ fraggenescan 1.31 (0/1) (1/1) (1/1) True True +gecko 112 112 gecko 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 1.2 gecko 1.2 (0/1) (1/1) (1/1) True False +genomic_super_signature 11 11 genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment 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 1.2.0 bioconductor-genomicsupersignature 1.10.0 (0/1) (0/1) (1/1) True False +get_orfs_or_cdss 15 15 get_orfs_or_cdss 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 0.2.3 biopython 1.70 (0/1) (1/1) (1/1) True False +gfastats 418 418 gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.6 gfastats 1.3.6 (1/1) (1/1) (1/1) True False +gffread 680 680 gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis 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 0.12.7 gffread 0.12.7 (1/1) (1/1) (1/1) True False +goenrichment 321 321 goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment 2.0.1 goenrichment 2.0.1 (2/2) (2/2) (2/2) True True +goseq 1210 1210 goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq 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 1.50.0 bioconductor-goseq 1.54.0 (1/1) (1/1) (1/1) True True +graphlan 247 247 graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees To update https://bitbucket.org/nsegata/graphlan/overview Metagenomics, Graphics, Phylogenetics graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ graphlan 1.1.3 (2/2) (2/2) (2/2) True True +gubbins 145 145 gubbins Gubbins - bacterial recombination detection gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins 3.2.1 gubbins 3.3.1 (1/1) (1/1) (1/1) True True +hapog 36 36 hapog Hapo-G - Haplotype-Aware Polishing of Genomes To update https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog 1.3.6 hapog 1.3.7 (0/1) (0/1) (1/1) True False +hardklor 2 2 hardklor, kronik Hardklör To update Proteomics hardklor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 (0/2) (0/2) (2/2) True False +hcluster_sg 13 13 hcluster_sg 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 0.5.1.1 hcluster_sg 0.5.1 (0/1) (0/1) (1/1) True False +hcluster_sg_parser 7 7 hcluster_sg_parser 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 0.2.1 (0/1) (0/1) (1/1) True False +heinz 54 54 heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. bionet BioNet 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. Protein interaction analysis Molecular interactions, pathways and networks, Protein interactions To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz 1.0 bioconductor-bionet 1.62.0 (4/4) (4/4) (4/4) True False +helixer 1 1 helixer 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 0.3.2 (0/1) (0/1) (1/1) True False +hifiasm 297 297 hifiasm 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 0.19.8 hifiasm 0.19.8 (1/1) (1/1) (1/1) True False +hifiasm_meta 12 12 hifiasm_meta A hifiasm fork for metagenome assembly using 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 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) True True +hisat2 4183 4183 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 2.2.1 hisat2 2.2.1 (1/1) (1/1) (1/1) True False +htseq_count 1419 1419 htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis To update 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 0.9.1+galaxy1 htseq 2.0.5 (1/1) (1/1) (1/1) True False +humann 247 247 humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann 3.8 humann 3.8 (6/13) (6/13) (13/13) True True +hypo 39 39 hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo 1.0.3 hypo 1.0.3 (0/1) (0/1) (1/1) True True +idba_ud 43 43 idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly 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 idba 1.1.3 (3/3) (0/3) (3/3) True True +idconvert 4 4 idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert proteowizard 3_0_9992 (0/1) (0/1) (1/1) True False +idr 30 30 idr 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/ 2.0.3 idr 2.0.4.2 (1/1) (0/1) (1/1) True False +iedb_api 12 12 iedb_api 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 2.15.2 python (0/1) (0/1) (1/1) True False +instagraal 14 14 instagraal Large genome reassembly based on Hi-C data instagraal instaGRAAL 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) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 (0/1) (0/1) (1/1) True False +intarna 23 23 intarna 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 3.3.2 intarna 3.3.2 (0/1) (0/1) (1/1) True False +integron_finder 58 58 integron_finder """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""" integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis To update https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder 2.0.2 hmmer 3.4 (0/1) (1/1) (1/1) True False +interproscan 677 677 interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 (1/1) (1/1) (1/1) True True +iqtree 681 681 iqtree 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/ 2.1.2 iqtree 2.2.6 (1/1) (1/1) (1/1) True True +isescan 50 50 isescan """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.""" ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan 1.7.2.3 isescan 1.7.2.1 (0/1) (1/1) (1/1) True False +isoformswitchanalyzer 29 29 isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR 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. Sequence comparison, Sequence analysis Computational biology, Gene transcripts 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 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 (1/1) (1/1) (1/1) True False +isoplot 1 1 isoplot 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 1.3.0+galaxy1 isoplot 1.3.1 (0/1) (0/1) (1/1) True False +itsx 38 38 itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 (0/1) (0/1) (1/1) True True +jbrowse 2269 2269 jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse 1.16.11 jbrowse 1.16.11 (2/2) (2/2) (2/2) True True +jcvi_gff_stats 255 255 jcvi_gff_stats 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 0.8.4 jcvi 1.3.9 (1/1) (1/1) (1/1) True False +jellyfish 91 91 jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish kmer-jellyfish 2.3.0 (0/1) (1/1) (1/1) True True +kc-align 19 19 kc-align Kc-Align custom tool kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping 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 1.0.2 kcalign 1.0.2 (1/1) (0/1) (1/1) True True +kleborate 38 38 kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate 2.3.2 kleborate 2.3.2 (0/1) (0/1) (1/1) True True +kofamscan 33 33 kofamscan 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 1.3.0 kofamscan 1.3.0 (0/1) (0/1) (1/1) True True +kraken 404 404 kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken 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/ kraken 1.1.1 (5/5) (5/5) (5/5) True True +kraken2 2367 2367 kraken2 Kraken2 for taxonomic designation. To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) True True +kraken_biom 182 182 kraken_biom 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 1.2.0 kraken-biom 1.2.0 (0/1) (1/1) (1/1) True True +kraken_taxonomy_report 354 354 kraken_taxonomy_report 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 0.0.3 biopython 1.70 (1/1) (0/1) (1/1) True True +legsta 7 7 legsta 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 0.5.1 legsta 0.5.1 (0/1) (0/1) (1/1) True True +length_and_gc_content 322 322 length_and_gc_content 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 0.1.2 r-optparse 1.3.2 (1/1) (1/1) (1/1) True False +lfq_protein_quant 3 3 lfq_protein_quant 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 1.0 bioconductor-msnbase 2.28.1 (0/1) (0/1) (1/1) True False +lighter 9 9 lighter 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 1.0 lighter 1.1.2 (0/1) (0/1) (1/1) True True +limma_voom 1012 1012 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics To update 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 3.50.1 bioconductor-limma 3.58.1 (1/1) (1/1) (1/1) True False +lineagespot 2 2 lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation 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 1.4.0 r-base (0/1) (0/1) (1/1) True True +links 77 77 links Scaffold genome assemblies with long reads. links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links 2.0.1 links 2.0.1 (0/1) (1/1) (1/1) True False +lotus2 114 114 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection Metagenomics To update http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.30 lotus2 2.32 (0/1) (0/1) (1/1) True True +maaslin2 29 29 maaslin2 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 0.99.12 maaslin2 0.99.12 (0/1) (0/1) (1/1) True True +maker 419 419 maker, maker_map_ids 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. maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker 2.31.11 maker 3.01.03 (2/2) (2/2) (2/2) True True +map_peptides_to_bed 1 1 map_peptides_to_bed 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 0.2 biopython 1.70 (0/1) (0/1) (1/1) True False +mapseq 2 2 mapseq 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 2.1.1 perl (0/1) (0/1) (1/1) True True +masigpro 13 13 masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro maSigPro 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. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq 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 1.49.3 coreutils 8.25 (1/1) (0/1) (1/1) True False +maxbin2 118 118 maxbin2 clusters metagenomic contigs into bins maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology 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/ maxbin2 2.2.7 (1/1) (1/1) (1/1) True True +maxquant 380 380 maxquant, maxquant_mqpar 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 2.0.3.0 maxquant 2.0.3.0 (2/2) (2/2) (2/2) True False +mcl 10 10 mcl_clustering Markov Cluster Algorithm To update http://micans.org/mcl/ Sequence Analysis, Metagenomics mcl bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mcl 14.137 mcl 22.282 (0/1) (0/1) (0/1) True True +mcl 10 10 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl 22.282 mcl 22.282 (0/1) (0/1) (1/1) True True +mea 3 3 mea 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 0.6.4.1 mea 0.6.4 (0/1) (0/1) (1/1) True False +megahit 548 548 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit 1.2.9 megahit 1.2.9 (1/1) (1/1) (1/1) True True +megahit_contig2fastg 54 54 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly 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 1.1.3 megahit 1.2.9 (1/1) (0/1) (1/1) True True +merqury 244 244 merqury Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury 1.3 merqury 1.3 (1/1) (1/1) (1/1) True True +meryl 350 350 meryl Meryl a k-mer counter. meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl 1.3 merqury 1.3 (1/1) (1/1) (1/1) True True +meta_proteome_analyzer 10 10 meta_proteome_analyzer 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 2.0.0 mpa-portable 2.0.0 (0/1) (0/1) (1/1) True False +metabat2 154 154 metabat2_jgi_summarize_bam_contig_depths, metabat2 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. MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ 2.15 metabat2 2.15 (1/2) (1/2) (2/2) True True +metagene_annotator 115 115 metagene_annotator 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 1.0.0 metagene_annotator 1.0 (0/1) (0/1) (1/1) True True +metanovo 15 15 metanovo 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 1.9.4 metanovo 1.9.4 (0/1) (0/1) (1/1) True False +metaphlan 427 427 customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ 4.0.6 metaphlan 4.0.6 (1/4) (2/4) (4/4) True True +metilene 103 103 metilene Differential DNA methylation calling To update RNA, Statistics metilene rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 (1/1) (1/1) (1/1) True False +migmap 7 7 migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap 1.0.3 migmap 1.0.3 (1/1) (0/1) (1/1) True False +minced 53 53 minced 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 0.2.0 minced 0.4.2 (0/1) (0/1) (1/1) True False +minia 109 109 minia Short-read assembler based on a de Bruijn graph minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia 3.2.6 minia 3.2.6 (0/1) (1/1) (1/1) True True +miniasm 178 178 miniasm 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 0.3_r179 miniasm 0.3 (1/1) (1/1) (1/1) True True +minipolish 21 21 minipolish Polishing miniasm assemblies minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 (0/1) (0/1) (1/1) True True +miniprot 15 15 miniprot, miniprot_index 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 0.12 miniprot 0.12 (0/2) (0/2) (2/2) True True +miranda 41 41 miranda 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 3.3a+galaxy1 miranda 3.3a (0/1) (0/1) (1/1) True False +mirnature 4 4 mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature iuc https://github.com/Bierinformatik/miRNAture 1.1 mirnature 1.1 (0/1) (0/1) (1/1) True False +mitobim 66 66 mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim 1.9.1 mitobim 1.9.1 (0/1) (1/1) (1/1) True False +mitohifi 56 56 mitohifi 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 3 (1/1) (0/1) (1/1) True False +mitos 58 58 mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos 1.1.4 mitos 2.1.6 (1/2) (1/2) (2/2) True True +mlst 570 570 mlst, mlst_list Scan contig files against PubMLST typing schemes mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Taxonomic classification Immunoproteins, genes and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst 2.22.0 mlst 2.23.0 (2/2) (2/2) (2/2) True True +morpheus 4 4 morpheus Morpheus MS Search Application To update Proteomics morpheus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 2.255.0 morpheus 287 (0/1) (1/1) (1/1) True False +mqc 5 5 mqc 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/ 1.9 mqc 1.10 (0/1) (0/1) (1/1) True False +msconvert 189 189 msconvert 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 3.0.20287 (1/1) (1/1) (1/1) True False +msgfplus 5 5 msgfplus MSGF+ To update Proteomics msgfplus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2023.01.1202 (0/1) (0/1) (1/1) True False +msms_extractor 1 1 msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor galaxyp 1.0.0 proteowizard 3_0_9992 (0/1) (0/1) (1/1) True False +msstats 144 144 msstats 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 4.0.0 bioconductor-msstats 4.10.0 (1/1) (1/1) (1/1) True False +msstatstmt 71 71 msstatstmt 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 2.0.0 bioconductor-msstatstmt 2.10.0 (0/1) (1/1) (1/1) True False +mt2mq 19 19 mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq galaxyp 1.1.0 r-tidyverse (0/1) (0/1) (1/1) True False +multigsea 2 2 multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules To update https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea 1.8.0 bioconductor-multigsea 1.12.0 (0/1) (0/1) (1/1) True True +multiqc 8320 8320 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation Sequencing, Bioinformatics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc 1.11 multiqc 1.19 (1/1) (1/1) (1/1) True True +mz_to_sqlite 33 33 mz_to_sqlite 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 2.1.1+galaxy0 mztosqlite 2.1.1 (1/1) (1/1) (1/1) True False +nanoplot 2195 2195 nanoplot 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/ 1.41.0 nanoplot 1.42.0 (1/1) (1/1) (1/1) True True +necat 95 95 necat Error correction and de-novo assembly for ONT Nanopore reads necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 (0/1) (0/1) (1/1) True False +nextclade 169 169 nextalign, nextclade 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 2.7.0 nextalign 2.14.0 (1/2) (1/2) (2/2) True True +nextdenovo 84 84 nextdenovo String graph-based de novo assembler for long reads nextdenovo NextDenovo "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." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 (0/1) (0/1) (1/1) True True +nonpareil 5 5 nonpareil 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 3.1.1 nonpareil 3.4.1 (1/1) (0/1) (1/1) True True +novoplasty 162 162 novoplasty 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 4.3.1 novoplasty 4.3.3 (0/1) (1/1) (1/1) True False +obisindicators 4 4 obisindicators, obis_data 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 0.0.2 r-base (1/2) (0/2) (1/2) True True +optitype 24 24 optitype 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 1.3.5 optitype 1.3.5 (0/1) (0/1) (1/1) True False +orfipy 53 53 orfipy Galaxy wrapper for ORFIPY orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy 0.0.4 orfipy 0.0.4 (1/1) (0/1) (1/1) True True +pangolin 259 259 pangolin 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 1.1.14 pangolin 4.3 (1/1) (1/1) (1/1) True False +pangolin 259 259 pangolin 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 4.3 pangolin 4.3 (1/1) (1/1) (1/1) True False +paralyzer 7 7 paralyzer 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 1.5 paralyzer 1.5 (0/1) (0/1) (1/1) True False +parse_mito_blast 31 31 parse_mito_blast 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 1.0.2 parse_mito_blast 1.0.2 (1/1) (1/1) (1/1) True False +pathview 565 565 pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview 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. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation 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 1.34.0 bioconductor-pathview 1.42.0 (1/1) (1/1) (1/1) True False +peakachu 78 78 peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu rnateam https://github.com/tbischler/PEAKachu 0.2.0+galaxy1 peakachu 0.2.0 (0/1) (0/1) (1/1) True False +pep_pointer 9 9 pep_pointer 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 0.1.3+galaxy1 python (1/1) (1/1) (1/1) True False +pepquery 23 23 pepquery 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 1.6.2 pepquery 2.0.2 (0/1) (0/1) (1/1) True False +pepquery2 10 10 pepquery2, pepquery2_index, pepquery2_show_sets 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 2.0.2 pepquery 2.0.2 (0/3) (0/3) (3/3) True False +peptide_genomic_coordinate 9 9 peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate galaxyp 1.0.0 python (1/1) (1/1) (1/1) True False +percolator 2 2 batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator Up-to-date Proteomics percolator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator 3.5 percolator 3.5 (0/4) (4/4) (4/4) True False +pfamscan 19 19 pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis 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 1.6 pfam_scan 1.6 (1/1) (1/1) (1/1) True True +pharokka 74 74 pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes " + pharokka + " To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " + pharokka + " (0/1) (1/1) (1/1) True True +phyml 104 104 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1) True True +pipmir 21 21 pipmir 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 0.1.0 pipmir 1.1 (0/1) (0/1) (1/1) True False +piranha 39 39 piranha 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 1.2.1.0 piranha 1.2.1 (0/1) (0/1) (1/1) True False +plasmidfinder 8 8 plasmidfinder """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 PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 (0/1) (0/1) (1/1) True True +plotly_ml_performance_plots 71 71 plotly_ml_performance_plots 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 0.2 pandas (1/1) (1/1) (1/1) True False +plotly_parallel_coordinates_plot 37 37 plotly_parallel_coordinates_plot 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 0.2 python (1/1) (1/1) (1/1) True False +plotly_regression_performance_plots 79 79 plotly_regression_performance_plots 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 0.1 python (1/1) (1/1) (1/1) True False +poisson2test 6 6 poisson2test 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 1.0.0 taxonomy 0.9.0 (0/1) (1/1) (1/1) True False +polypolish 24 24 polypolish """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 Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish 0.5.0 polypolish 0.6.0 (0/1) (0/1) (1/1) True False +prinseq 70 70 prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ @TOOL_VERSION+galaxy2 prinseq 0.20.4 (1/1) (0/1) (1/1) True False +progressivemauve 249 249 progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update Sequence Analysis progressivemauve iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve progressivemauve snapshot_2015_02_13 (2/2) (0/2) (2/2) True False +prokka 3233 3233 prokka Rapid annotation of prokaryotic genomes prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ 1.14.6 prokka 1.14.6 (1/1) (1/1) (1/1) True True +proteinortho 125 125 proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Homology-based gene prediction Phylogeny To update https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho 6.2.3 proteinortho 6.3.1 (0/3) (0/3) (3/3) True True +proteomiqon_joinquantpepionswithproteins 4 4 proteomiqon_joinquantpepionswithproteins 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 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 (0/1) (0/1) (1/1) True False +proteomiqon_labeledproteinquantification 5 5 proteomiqon_labeledproteinquantification 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 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 (0/1) (0/1) (1/1) True False +proteomiqon_labelfreeproteinquantification 3 3 proteomiqon_labelfreeproteinquantification 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 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 (0/1) (0/1) (1/1) True False +proteomiqon_mzmltomzlite 5 5 proteomiqon_mzmltomzlite 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 0.0.8 proteomiqon-mzmltomzlite 0.0.8 (0/1) (0/1) (1/1) True False +proteomiqon_peptidedb 6 6 proteomiqon_peptidedb 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 0.0.7 proteomiqon-peptidedb 0.0.7 (0/1) (0/1) (1/1) True False +proteomiqon_peptidespectrummatching 4 4 proteomiqon_peptidespectrummatching 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 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 (0/1) (0/1) (1/1) True False +proteomiqon_proteininference 4 4 proteomiqon_proteininference 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 0.0.7 proteomiqon-proteininference 0.0.7 (0/1) (0/1) (1/1) True False +proteomiqon_psmbasedquantification 4 4 proteomiqon_psmbasedquantification 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 0.0.8 proteomiqon-psmbasedquantification 0.0.9 (0/1) (0/1) (1/1) True False +proteomiqon_psmstatistics 4 4 proteomiqon_psmstatistics 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 0.0.8 proteomiqon-psmstatistics 0.0.8 (0/1) (0/1) (1/1) True False +pureclip 36 36 pureclip 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 1.0.4 pureclip 1.3.1 (0/1) (0/1) (1/1) True False +purge_dups 167 167 purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups 1.2.6 purge_dups 1.2.6 (1/1) (1/1) (1/1) True False +pycoqc 350 350 pycoqc 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 2.5.2 pycoqc 2.5.2 (1/1) (1/1) (1/1) True True +quantp 6 6 quantp Correlation between protein and transcript abundance To update Proteomics quantp galaxyp 1.1.2 r-data.table 1.11.6 (0/1) (0/1) (1/1) True False +quantwiz_iq 1 1 quantwiz_iq 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 2.0 quantwiz-iq 2.0 (0/1) (0/1) (1/1) True False +quast 3567 3567 quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast 5.2.0 quast 5.2.0 (1/1) (1/1) (1/1) True True +racon 309 309 racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon 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 Genome assembly, Mapping assembly, Sequence trimming Whole genome sequencing, Sequence assembly, Plant biology Up-to-date https://github.com/isovic/racon Sequence Analysis racon bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 (1/1) (1/1) (1/1) True True +ragtag 237 237 ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag 2.1.0 ragtag 2.1.0 (0/1) (0/1) (1/1) True False +rapidnj 14 14 rapidnj Galaxy wrapper for the RapidNJ tool rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj 2.3.2 rapidnj 2.3.2 (1/1) (0/1) (1/1) True False +raven 262 262 raven 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 1.8.0 raven-assembler 1.8.3 (0/1) (1/1) (1/1) True False +rawtools 14 14 rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 (0/1) (1/1) (1/1) True False +raxml 383 383 raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml 8.2.12 raxml 8.2.13 (1/1) (1/1) (1/1) True True +rcas 38 38 rcas 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/ 1.5.4 bioconductor-rcas 1.28.2 (0/1) (0/1) (1/1) True False +read_it_and_keep 71 71 read_it_and_keep 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 0.2.2 read-it-and-keep 0.3.0 (1/1) (0/1) (1/1) True True +recentrifuge 48 48 recentrifuge """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.""" Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing To update https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge 1.12.1 recentrifuge 1.13.2 (0/1) (0/1) (1/1) True True +red 88 88 red 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 2018.09.10 red 2018.09.10 (1/1) (1/1) (1/1) True False +remurna 2 2 remurna 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 1.0.0 remurna 1.0 (0/1) (0/1) (1/1) True False +repeatmodeler 217 217 repeatmodeler 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 2.0.5 (1/1) (1/1) (1/1) True False +rnasnp 5 5 rnasnp 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 1.2.0 rnasnp 1.2 (0/1) (0/1) (1/1) True False +rnaz 14 14 rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window 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 2.1.1 rnaz 2.1.1 (0/6) (0/6) (6/6) True False +roary 656 656 roary Roary the pangenome pipeline roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary 3.13.0 roary 3.13.0 (1/1) (1/1) (1/1) True True +ruvseq 76 76 ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq 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 1.26.0 bioconductor-ruvseq 1.36.0 (1/1) (0/1) (1/1) True False +sailfish 55 55 sailfish 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 0.10.1.1 bzip2 (1/1) (1/1) (1/1) True False +salmon 746 746 alevin, salmon, salmonquantmerge 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 1.10.1 salmon 1.10.2 (2/3) (1/3) (3/3) True True +sample_seqs 149 149 sample_seqs 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 0.2.6 biopython 1.70 (1/1) (1/1) (1/1) True False +samtools_depth 296 296 samtools_depth 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 0.0.3 samtools 1.19 (1/1) (0/1) (1/1) True False +samtools_idxstats 1450 1450 samtools_idxstats 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 0.0.6 samtools 1.19 (1/1) (1/1) (1/1) True False +sarscov2formatter 7 7 sarscov2formatter 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 1.0 sarscov2formatter 1.0 (1/1) (0/1) (1/1) True True +sarscov2summary 1 1 sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary 0.1 sarscov2summary 0.5 (1/1) (0/1) (1/1) True True +scoary 61 61 scoary 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 1.6.16 scoary 1.6.16 (0/1) (0/1) (1/1) True True +scpipe 11 11 scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scPipe 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. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-seq, Sequencing 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 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 (1/1) (0/1) (1/1) True False +selectsequencesfrommsa 27 27 selectsequencesfrommsa 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 1.0.5 selectsequencesfrommsa 1.0.5 (0/1) (0/1) (1/1) True False +semibin 10 10 semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Up-to-date https://semibin.readthedocs.io/en/latest/ Metagenomics semibin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin 2.0.2 semibin 2.0.2 (0/6) (0/6) (6/6) True True +seq2hla 16 16 seq2hla Precision HLA typing and expression from RNAseq data seq2hla Seq2HLA 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. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla 2.3 seq2hla 2.3 (0/1) (0/1) (1/1) True False +seq_composition 71 71 seq_composition 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 0.0.5 biopython 1.70 (1/1) (0/1) (1/1) True False +seq_filter_by_id 306 306 seq_filter_by_id 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 0.2.9 biopython 1.70 (1/1) (1/1) (1/1) True False +seq_filter_by_mapping 82 82 seq_filter_by_mapping 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 0.0.8 biopython 1.70 (0/1) (0/1) (1/1) True False +seqcomplexity 16 16 seqcomplexity 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/ 0.1.2 seqcomplexity 0.1.2 (1/1) (0/1) (1/1) True False +seurat 66 66 seurat 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 4.3.0.1 r-seurat 3.0.2 (1/1) (1/1) (1/1) True False +seurat 66 66 seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_normalise_data, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_scale_data De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.3.0 seurat-scripts 4.0.0 (0/13) (0/13) (12/13) True False +shasta 154 154 shasta 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 0.6.0 shasta 0.11.1 (0/1) (1/1) (1/1) True False +shovill 1008 1008 shovill Faster de novo assembly pipeline based around Spades shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill 1.1.0 shovill 1.1.0 (1/1) (1/1) (1/1) True True +sickle 269 269 sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle 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. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle 1.33.2 sickle-trim 1.33 (1/1) (0/1) (1/1) True False +sina 42 42 sina SINA reference based multiple sequence alignment sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina 1.7.2 sina 1.7.2 (1/1) (0/1) (1/1) True False +sistr_cmd 133 133 sistr_cmd SISTR in silico serotyping tool Up-to-date https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd nml 1.1.1 sistr_cmd 1.1.1 (0/1) (1/1) (1/1) True True +slamdunk 2 2 alleyoop, slamdunk 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 0.4.3 slamdunk 0.4.3 (2/2) (0/2) (2/2) True False +sleuth 8 8 sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth 0.30.1 r-sleuth 0.30.1 (0/1) (0/1) (1/1) True False +smudgeplot 22 22 smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Up-to-date https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot galaxy-australia https://github.com/galaxyproject/tools-iuc 0.2.5 smudgeplot 0.2.5 (1/1) (1/1) (1/1) True False +sniffles 58 58 sniffles Galaxy wrapper for sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing To update https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles iuc https://github.com/galaxyproject/tools-iuc 1.0.12 sniffles 2.2 (1/1) (1/1) (1/1) True False +snipit 22 22 snipit Summarise snps relative to a reference sequence To update https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit 1.0.7 snipit 1.2 (0/1) (0/1) (1/1) True False +snippy 1035 1035 snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy snippy 4.6.0 (3/3) (3/3) (3/3) True True +socru 13 13 socru 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 2.1.7 socru 2.2.4 (1/1) (0/1) (1/1) True False +sonneityping 1 1 sonneityping 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 20210201 sonneityping 20210201 (0/1) (0/1) (1/1) True True +spades 2309 2309 spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades 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. Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades 3.15.5 spades 3.15.5 (9/9) (9/9) (9/9) True True +spaln 34 34 list_spaln_tables, spaln 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 2.4.9 python (2/2) (0/2) (2/2) True False +spotyping 12 12 spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation 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 2.1 spotyping 2.1 (0/1) (0/1) (1/1) True True +srst2 22 22 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml 0.3.7 srst2 0.2.0 (0/1) (0/1) (1/1) True True +srst2 22 22 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens To update http://katholt.github.io/srst2/ Metagenomics srst2 iuc https://github.com/katholt/srst2 0.2.0 samtools 1.19 (0/1) (0/1) (1/1) True True +sshmm 5 5 sshmm 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/ 1.0.7 sshmm 1.0.7 (0/1) (0/1) (1/1) True False +star_fusion 35 35 star_fusion 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 0.5.4-3+galaxy1 star-fusion 1.12.0 (1/1) (1/1) (1/1) True False +structure 59 59 structure for using multi-locus genotype data to investigate population structure. structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure 2.3.4 structure 2.3.4 (0/1) (0/1) (1/1) True True +syndiva 2 2 syndiva 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 1.0 clustalo 1.2.4 (0/1) (0/1) (1/1) True False +t2t_report 26 26 t2t_report 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 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) True True +t_coffee 70 70 t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b (0/1) (0/1) (1/1) True False +targetfinder 37 37 targetfinder 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/ 1.7 targetfinder 1.7 (1/1) (1/1) (1/1) True False +taxonomy_krona_chart 1801 1801 taxonomy_krona_chart Krona pie chart from taxonomic profile krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 (1/1) (1/1) (1/1) True True +tbl2gff3 229 229 tbl2gff3 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 1.2 bcbiogff 0.6.6 (0/1) (1/1) (1/1) True False +te_finder 7 7 te_finder Transposable element insertions finder tefinder TEfinder 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. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ 1.0.1 samtools 1.19 (0/1) (0/1) (1/1) True False +tetyper 8 8 tetyper 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 1.1 tetyper 1.1 (1/1) (0/1) (1/1) True False +tgsgapcloser 36 36 tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 (0/1) (0/1) (1/1) True False +tn93 7 7 tn93_readreduce, tn93, tn93_cluster, tn93_filter 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/ 1.0.6 tn93 1.0.13 (4/4) (0/4) (4/4) True False +tophat2 312 312 tophat2 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 2.1.1 bowtie2 2.5.3 (1/1) (1/1) (1/1) True False +transdecoder 348 348 transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder 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. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder 5.5.0 transdecoder 5.7.1 (1/1) (1/1) (1/1) True False +translate_bed 49 49 translate_bed 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 0.1.0 (1/1) (1/1) (1/1) True False +translate_bed_sequences 6 6 translate_bed_sequences 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 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) True False +transtermhp 5 5 transtermhp Finds rho-independent transcription terminators in bacterial genomes To update Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp transtermhp 2.09 (1/1) (0/1) (1/1) True True +trim_galore 2334 2334 trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming Sequence analysis 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 0.6.7 trim-galore 0.6.10 (1/1) (1/1) (1/1) True True +trinity 678 678 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity Trinity 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. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity 2.15.1 trinity 2.15.1 (8/13) (11/13) (13/13) True False +trinotate 151 151 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate 3.2.2 trinotate 4.0.2 (1/1) (1/1) (1/1) True False +unicycler 1558 1558 unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler 0.5.0 unicycler 0.5.0 (1/1) (1/1) (1/1) True True +unipept 115 115 unipept Unipept retrieves metaproteomics information To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept galaxyp https://unipept.ugent.be/apidocs 4.5.1 python (1/1) (1/1) (1/1) True False +uniprotxml_downloader 79 79 uniprotxml_downloader 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 2.4.0 requests (0/1) (1/1) (1/1) True False +usher 5 5 usher_matutils, usher UShER toolkit wrappers To update https://github.com/yatisht/usher Phylogenetics usher iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher 0.2.1 usher 0.6.3 (0/2) (0/2) (2/2) True True +valet 20 20 valet 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 valet 1.0 (1/1) (0/1) (1/1) True True +validate_fasta_database 25 25 validate_fasta_database 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 0.1.5 validate-fasta-database 1.0 (0/1) (0/1) (1/1) True False +vapor 94 94 vapor Classify Influenza samples from raw short read sequence data vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor 1.0.2 vapor 1.0.2 (1/1) (0/1) (1/1) True True +venn_list 248 248 venn_list 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 0.1.2 galaxy_sequence_utils 1.1.5 (1/1) (0/1) (1/1) True False +verkko 9 9 verkko 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 1.3.1 verkko 1.4.1 (0/1) (0/1) (1/1) True False +volcanoplot 1749 1749 volcanoplot Tool to create a Volcano Plot To update Visualization, Transcriptomics, Statistics volcanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot 0.0.5 r-ggplot2 2.2.1 (1/1) (1/1) (1/1) True False +wtdbg 116 116 wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 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. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 (0/1) (0/1) (1/1) True True +yahs 64 64 yahs 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 1.2a.2 yahs 1.2a.2 (1/1) (1/1) (1/1) True False diff --git a/results/microgalaxy/tools_wordcloud.png b/results/microgalaxy/tools_wordcloud.png new file mode 100644 index 00000000..9c895452 Binary files /dev/null and b/results/microgalaxy/tools_wordcloud.png differ