From e3c3d664e42a48aea80a2c81109214e253469466 Mon Sep 17 00:00:00 2001 From: Alexandre Cormier Date: Sun, 3 Jul 2022 19:18:20 +0200 Subject: [PATCH] update to v4 --- test/Softwares.csv | 774 +++++++++++++++++++++++++-------------------- 1 file changed, 431 insertions(+), 343 deletions(-) diff --git a/test/Softwares.csv b/test/Softwares.csv index 947ed09..3a9c154 100644 --- a/test/Softwares.csv +++ b/test/Softwares.csv @@ -1,343 +1,431 @@ -Name,EDAM,Environment,Topic,Access,Doc,Description,Path -"ABCtoolbox - 2.0","statistical-inference","shell","Other","Cmdline only","https://bitbucket.org/phaentu/abctoolbox-public/wiki/Home","a general-purpose program to perform Approximate Bayesian Computation","/path/to/abctoolbox/2.0" -"abricate - 0.9.8","gene-prediction","conda","Metagenomics","Galaxy and cmdline","https://github.com/tseemann/abricate","Mass screening of contigs for antibiotic resistance genes","/path/to/abricate/0.9.8" -"ANGSD - 0.923","genotyping","conda","Epigenetics","Cmdline only","http://www.popgen.dk/angsd/index.php/ANGSD","Analysis of next generation Sequencing Data","/path/to/angsd/0.923" -"ANGSD - 0.931","genotyping","conda","Genomics","Cmdline only","http://www.popgen.dk/angsd/index.php/ANGSD","Analysis of next generation Sequencing Data","/path/to/angsd/0.931" -"anvi'o - 4","visualisation,workflows","conda","Metabarcoding","Cmdline only","http://merenlab.org/software/anvio/","advanced analysis and visualization platform for omics data","/path/to/anvio/4" -"anvi'o - 5.1.0","visualisation,workflows","conda","Metabarcoding","Cmdline only","http://merenlab.org/software/anvio/","advanced analysis and visualization platform for omics data","/path/to/anvio/5" -"anvi'o - 6","visualisation,workflows","conda","Transcriptomics","Cmdline only","http://merenlab.org/software/anvio/","advanced analysis and visualization platform for omics data","/path/to/anvio/6" -"ARB - 6.0.6","visualisation,phylogenetic-analysis","conda","Genomics","Cmdline only","http://www.arb-home.de/documentation.html","Silva visualization tool","/path/to/arb/6.0.6" -"ARCS - 1.0.5","genome-assembly,scaffolding","conda","Genomics","Cmdline only","https://github.com/bcgsc/arcs/tree/v1.0.5","Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data.","/path/to/arcs/1.0.5" -"ARLSUMSTAT - 3.5.2","statistics-and-probability","shell","Multi-thematic","Cmdline only","http://cmpg.unibe.ch/software/arlequin35/man/arlsumstat_readme.txt","modified version of Arlequin for computing summary statistics","/path/to/arlsumstat/3.5.2" -"AUGUSTUS - 3.3","gene-prediction","conda","Other","Cmdline only","http://augustus.gobics.de/","gene prediction program for eukaryotes","/path/to/augustus/3.3" -"Bam - 0.5.1","data-handling","conda","Genomics","Cmdline only","https://matricks.github.io/bam/bam.html","Bam is a build system with the focus on being having fast build times and flexiable build scripts","/path/to/bam/0.5.1" -"bam2fastq - 1.1.0","data-handling","conda","Metabarcoding","Cmdline only","https://github.com/jts/bam2fastq","Simple convertor from bam to FASTQ ","/path/to/bam2fastq/1.1.0" -"bam2fastx - 1.3.0","data-handling","conda","Multi-thematic","Cmdline only","https://github.com/PacificBiosciences/bam2fastx","Conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data","/path/to/bam2fastx/1.3.0" -"BamTools - 2.5.1","data-handling","conda","Other","Cmdline only","https://github.com/pezmaster31/bamtools","Both a programmer's API and an end-user's toolkit for handling BAM files","/path/to/bamtools/2.5.1" -"bamUtil - 1.0.14","data-handling","conda","Metabarcoding","Cmdline only","https://github.com/statgen/bamUtil","repository that contains several programs that perform operations on SAM/BAM files","/path/to/bamutil/1.0.14" -"Bandage - 0.8.1","sequence-visualisation","conda","Transcriptomics","Cmdline only","https://github.com/rrwick/Bandage","a Bioinformatics Application for Navigating De novo Assembly Graphs Easily","/path/to/bandage/0.8.1" -"BaseSpace CLI - 1.0.0","data-handling","shell","Genomics","Cmdline only","https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview","scripting and programmatic access to Illumina BaseSpace Sequence Hub","/path/to/BaseSpaceCLI/1.0.0" -"bbmap - 38.57","data-handling","conda","Multi-thematic","Cmdline only","https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/","A splice-aware global aligner for DNA and RNA sequencing reads","/path/to/bbmap/38.57" -"bbtools - 34.62","data-handling","conda","Genomics","Cmdline only","https://jgi.doe.gov/data-and-tools/bbtools/","BBMap short read aligner, and other bioinformatic tools (reads filter, reads merge, sequences converter) ","/path/to/bbtools/37.62" -"BCFtools - 1.10.2","data-handling","conda","Metagenomics","Galaxy and cmdline","https://samtools.github.io/bcftools/bcftools.html","Utilities for variant calling and manipulating VCFs and BCFs.","/path/to/bcftools/1.10.2" -"BCFtools - 1.4.1","data-handling","conda","Multi-thematic","Galaxy and cmdline","https://samtools.github.io/bcftools/bcftools.html","Utilities for variant calling and manipulating VCFs and BCFs.","/path/to/bcftools/1.4.1" -"Beagle - 4.0_06Jun17","genotyping","conda","Transcriptomics","Cmdline only","https://faculty.washington.edu/browning/beagle/b4_0.html","Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection","/path/to/beagle/4.0_06Jun17" -"BEDOPS - 2.4.38","workflows","conda","Genomics","Cmdline only","https://github.com/bedops/bedops","high-performance genomic feature operations","/path/to/bedops/2.4.38" -"bedtools - 2.26.0","data-handling","conda","Metagenomics","Cmdline only","http://bedtools.readthedocs.io/en/latest/","Toolset for genome arithmetic","/path/to/bedtools/2.26.0" -"bedtools - 2.27.1","data-handling","conda","Other","Cmdline only","http://bedtools.readthedocs.io/en/latest/","Toolset for genome arithmetic","/path/to/bedtools/2.27.1" -"BeeDeeM - 4.5.0","database-management","conda","Metabarcoding","Cmdline only","https://github.com/pgdurand/BeeDeeM/wiki","a Bioinformatics Databank Manager System","/path/to/beedeem/4.5.0" -"BeeDeeM-Tools - 2.0.0","data-handling","shell","Genomics","Cmdline only","https://gitlab.ifremer.fr/bioinfo/BeeDeeM-Tools/blob/master/documentation/tutorial.md","sequence-based data analysis pipeline tools","/path/to/beedeem-tools/2.0.0" -"BeeDeeM-Tools - 2.0.1","data-handling","shell","Multi-thematic","Cmdline only","https://gitlab.ifremer.fr/bioinfo/BeeDeeM-Tools/blob/master/documentation/tutorial.md","sequence-based data analysis pipeline tools","/path/to/beedeem-tools/2.0.1" -"Bioawk - 1.0","data-handling","conda","Genomics","Cmdline only","https://github.com/lh3/bioawk","Extension to Brian Kernighan's awk, adding the support of several common biological data formats","/path/to/bioawk/1.0" -"bioconductor-chromstaR - 1.8.1","chip-seq","conda","Transcriptomics","Cmdline only","https://bioconductor.org/packages/3.8/bioc/html/chromstaR.html","Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data","/path/to/bioconductor-chromstar/1.8.1" -"bioconductor-dada2 - 1.6.0","genetic-variation-analysis","conda","Transcriptomics","Cmdline only","https://bioconductor.org/packages/release/bioc/html/dada2.html","Accurate, high-resolution sample inference from amplicon sequencing data","/path/to/bioconductor-dada2/1.6" -"bioconductor-dada2 - 1.8.0","genetic-variation-analysis","conda","Other","Cmdline only","https://bioconductor.org/packages/release/bioc/html/dada2.html","Accurate, high-resolution sample inference from amplicon sequencing data","/path/to/bioconductor-dada2/1.8" -"biom-format - 2.1.6","conversion","conda","Metabarcoding","Galaxy and cmdline","http://biom-format.org/documentation/biom_conversion.html","Converting between file formats","/path/to/biom-format/2.1.6" -"Bioperl - 1.7.2","data-handling","conda","Epigenetics","Cmdline only","https://bioperl.org","Perl tools for comutational molecular biology","/path/to/bioperl/1.7.2" -"Biopython - 1.70","data-handling","conda","Epigenetics","Cmdline only","http://biopython.org/DIST/docs/tutorial/Tutorial.html","Python tools for comutational molecular biology","/path/to/biopython/1.70" -"Bismark - 0.17","bisulfite-mapping","conda","Other","Cmdline only","http://www.bioinformatics.babraham.ac.uk/projects/bismark/","A tool to map bisulfite converted sequence reads and determine cytosine methylation states","/path/to/bismark/0.17" -"Bismark - 0.19","bisulfite-mapping","conda","Multi-thematic","Cmdline only","http://www.bioinformatics.babraham.ac.uk/projects/bismark/","A tool to map bisulfite converted sequence reads and determine cytosine methylation states","/path/to/bismark/0.19" -"Bismark - 0.20.0","bisulfite-mapping","conda","Genomics","Galaxy and cmdline","http://www.bioinformatics.babraham.ac.uk/projects/bismark/","A tool to map bisulfite converted sequence reads and determine cytosine methylation states","/path/to/bismark/0.20.0" -"BisSNP - 0.82.2","methylation-calling","docker","Metagenomics","Cmdline only","http://people.csail.mit.edu/dnaase/bissnp2011/","Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller","/path/to/bissnp/0.82.2" -"BLASR - 5.3.3","read-mapping","conda","Genomics","Cmdline only","https://github.com/PacificBiosciences/blasr","BLASR: The PacBio long read aligner ","/path/to/blasr/5.3.3" -"BlastViewer - 5.2.0","sequence-similarity-search,visualisation","shell","Metabarcoding","Cmdline only","https://github.com/pgdurand/BlastViewer/wiki","A graphical workbench to analyse BLAST result files.","/path/to/blastviewer/5.2.0" -"blobtools - 1.1","visualisation,quality-control,taxonomic-partitioning","conda","Multi-thematic","Cmdline only","https://github.com/DRL/blobtools","A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets ","/path/to/blobtools/1.1" -"Bowtie 2 - 2.3.0","read-mapping","conda","Metabarcoding","Galaxy and cmdline","http://bowtie-bio.sourceforge.net/bowtie2/index.shtml","Aligning sequencing reads to long reference sequences","/path/to/bowtie2/2.3.0" -"Bowtie 2 - 2.3.4.1","read-mapping","conda","Multi-thematic","Cmdline only","http://bowtie-bio.sourceforge.net/bowtie2/index.shtml","Aligning sequencing reads to long reference sequences","/path/to/bowtie2/2.3.4.1" -"Bowtie 2 - 2.3.4.3","read-mapping","conda","Genomics","Galaxy and cmdline","http://bowtie-bio.sourceforge.net/bowtie2/index.shtml","Aligning sequencing reads to long reference sequences","/path/to/bowtie2/2.3.4.3" -"Bowtie 2 - 2.3.5","read-mapping","conda","Other","Galaxy and cmdline","http://bowtie-bio.sourceforge.net/bowtie2/index.shtml","Aligning sequencing reads to long reference sequences","/path/to/bowtie2/2.3.5" -"BRAKER - 2","gene-prediction","conda","Other","Cmdline only","https://github.com/Gaius-Augustus/BRAKER","fully automated training of the gene prediction tools GeneMark-EX","/path/to/braker/2" -"BS-SNPer - master","methylation-calling","docker","Genomics","Cmdline only","https://github.com/hellbelly/BS-Snper","Exploration of SNP sites from BS-Seq data","/path/to/bs-snper/master" -"bsmap - 2.90","bisulfite-mapping","conda","Transcriptomics","Galaxy and cmdline","https://code.google.com/archive/p/bsmap/","short reads mapping software for bisulfite sequencing reads","/path/to/bsmap/2.9" -"bsmapz - 1.1.1","bisulfite-mapping","conda","Genomics","Galaxy and cmdline","https://github.com/zyndagj/BSMAPz","short reads mapping software for bisulfite sequencing reads","/path/to/bsmapz/1.1.1" -"BUSCO - 3.0.2","sequence-assembly-validation","conda","Multi-thematic","Cmdline only","http://busco.ezlab.org/","Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs","/path/to/busco/3.0.2" -"BUSCO - 4.0.0","sequence-assembly-validation","conda","Genomics","Galaxy and cmdline","http://busco.ezlab.org/","Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs","/path/to/busco/4.0.0" -"BUSCO - 4.0.4","sequence-assembly-validation","conda","Other","Cmdline only","http://busco.ezlab.org/","Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs","/path/to/busco/4.0.4" -"BWA - 0.7.15","read-mapping","conda","Transcriptomics","Galaxy and cmdline","http://bio-bwa.sourceforge.net/","Mapping low-divergent sequences against a large reference genome","/path/to/bwa/0.7.15" -"Canu - 1.6","genome-assembly","conda","Multi-thematic","Cmdline only","http://canu.readthedocs.io","A single molecule sequence assembler for genomes large and small","/path/to/canu/1.6" -"Canu - 1.7","genome-assembly","conda","Transcriptomics","Cmdline only","http://canu.readthedocs.io","A single molecule sequence assembler for genomes large and small","/path/to/canu/1.7" -"Canu - 1.9","genome-assembly","conda","Epigenetics","Cmdline only","http://canu.readthedocs.io","A single molecule sequence assembler for genomes large and small","/path/to/canu/1.9" -"Canu - 2.0","genome-assembly","conda","Genomics","Cmdline only","http://canu.readthedocs.io","A single molecule sequence assembler for genomes large and small","/path/to/canu/2.0" -"cd-hit - 4.8.1","sequence-clustering","conda","Epigenetics","Galaxy and cmdline","http://weizhongli-lab.org/cd-hit/","clustering and comparing protein or nucleotide sequences","/path/to/cd-hit/4.8.1" -"Centrifuge - 1.0.3","taxonomic-classification","conda","Transcriptomics","Cmdline only","https://github.com/infphilo/centrifuge","Classifier for metagenomic sequences","/path/to/centrifuge/1.0.3" -"circos - 0.69.6","data-visualisation","conda","Metagenomics","Cmdline only","http://circos.ca","package for visualizing data and information. It visualizes data in a circular layout","/path/to/circos/0.69.6" -"Clustal Omega - 1.2.3","multiple-sequence-alignment","conda","Genomics","Galaxy and cmdline","http://www.clustal.org/omega/","Multiple sequence alignement","/path/to/clustalo/1.2.3" -"Clustal W - 2.1","multiple-sequence-alignment","conda","Multi-thematic","Galaxy and cmdline","http://www.clustal.org/omega/","Multiple alignment of nucleic acid and protein sequences ","/path/to/clustalw/2.1" -"CNVkit - 0.9.5","variant-calling","conda","Transcriptomics","Cmdline only","http://cnvkit.readthedocs.org","Copy number variant detection from targeted DNA sequencing","/path/to/cnvkit/0.9.5" -"Conda-BioPython - latest","data-handling","conda","Genomics","Cmdline only","https://docs.conda.io/en/latest/","Generic conda env. with BioPython","/path/to/biopython/1.76" -"CONSENT - 1.2","read-correction","shell","Other","Cmdline only","https://github.com/morispi/CONSENT","elf-correction method for long reads","/path/to/consent/1.2" -"CRISP - 0.7","variant-calling","conda","Epigenetics","Cmdline only","https://bansal-lab.github.io/software/crisp.html","Detect SNPs and short indels from high-throughput sequencing of pooled DNA samples","/path/to/crisp/0.7" -"cutadapt - 1.13","sequence-trimming","conda","Metagenomics","Galaxy and cmdline","https://cutadapt.readthedocs.io/en/stable/","Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads","/path/to/cutadapt/1.13" -"cutadapt - 1.16","sequence-trimming","conda","Metabarcoding","Galaxy and cmdline","https://cutadapt.readthedocs.io/en/stable/","Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads","/path/to/cutadapt/1.16" -"cutadapt - 1.18","sequence-trimming","conda","Metagenomics","Galaxy and cmdline","https://cutadapt.readthedocs.io/en/stable/","Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads","/path/to/bbmap/38.22" -"cutadapt - 2.8","sequence-trimming","conda","Other","Cmdline only","https://cutadapt.readthedocs.io/en/stable/","Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads","/path/to/cutadapt/2.8" -"dada2 - 1.10","community-profiling","conda","Genomics","Cmdline only","https://benjjneb.github.io/dada2/index.html","Fast and accurate sample inference from amplicon data with single-nucleotide resolution","/path/to/dada2/1.10" -"dbCAN2 - 2.0.6","sequence-annotation","shell","Multi-thematic","Cmdline only","https://github.com/linnabrown/run_dbcan","Tools to handle CAZyme annotation","/path/to/dbcan/2.0.6" -"DBG2OLC - 20160205","genome-assembly","conda","Epigenetics","Cmdline only","https://github.com/yechengxi/DBG2OLC","Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies","/path/to/dbg2olc/20160205" -"DBG2OLC - 20180222","genome-assembly","conda","Transcriptomics","Cmdline only","https://github.com/yechengxi/DBG2OLC","Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies","/path/to/dbg2olc/20180222" -"DESeq2 - 1.14.1","differential-gene-expression-analysis","conda","Other","Galaxy and cmdline","https://bioconductor.org/packages/release/bioc/html/DESeq2.html","Differential gene expression analysis based on the negative binomial distribution","/path/to/bioconductor-deseq2/1.14.1" -"DESeq2 - 1.20.0","differential-gene-expression-analysis","conda","Metagenomics","Galaxy and cmdline","https://bioconductor.org/packages/release/bioc/html/DESeq2.html","Differential gene expression analysis based on the negative binomial distribution","/path/to/bioconductor-deseq2/1.20.0" -"diamond - 0.9.24","sequence-similarity-search","shell","Transcriptomics","Cmdline only","https://github.com/bbuchfink/diamond","sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data","/path/to/diamond/0.9.24" -"DiscoSNP - 2.4.4","variant-calling","conda","Genomics","Cmdline only","https://gatb.inria.fr/software/discosnp/","Tool for discovering Single Nucleotide Polymorphism","/path/to/discosnp/2.4.4" -"DRAP - 1.91","genome-assembly","docker","Other","Cmdline only","http://www.sigenae.org/drap/","De novo RNA-seq Assembly Pipeline","/path/to/drap/1.91" -"dRep - 2.2.3","genome-alignment","conda","Other","Cmdline only","https://github.com/MrOlm/drep","dRep is a python program for rapidly comparing large numbers of genomes","/path/to/drep/2.2.3" -"eCAMI - master","sequence-annotation","conda","Multi-thematic","Cmdline only","https://github.com/zhanglabNKU/eCAMI","Simultaneous Classification and Motif Identification for enzyme/CAZyme annotation","/path/to/ecami/master" -"eggnog-mapper - 1.0.3","sequence-annotation","conda","Epigenetics","Cmdline only","http://eggnog-mapper.embl.de","Fast genome-wide functional annotation through orthology assignment","/path/to/eggnog-mapper/1.0.3" -"Eigensoft - 7.2.1","population-structure","conda","Metagenomics","Cmdline only","https://www.hsph.harvard.edu/alkes-price/software/","Analyze population structure and perform stratification correction","/path/to/eigensoft/7.2.1" -"EMBOSS - 6.5.7","data-handling","conda","Multi-thematic","Cmdline only","http://emboss.sourceforge.net/","Analysis package specially developed for the needs of the molecular biology","/path/to/emboss/6.5.7" -"fasta-splitter - 0.2.4","data-handling","conda","Other","Cmdline only","http://kirill-kryukov.com/study/tools/fasta-splitter/","Divides a large FASTA file into a set of smaller, approximately equally sized files","/path/to/fasta-splitter/0.2.4" -"FastANI - 1.3","sequence-alignment-similarity","conda","Genomics","Galaxy and cmdline","https://github.com/ParBLiSS/FastANI","Fast Whole-Genome Similarity (ANI) Estimation ","/path/to/fastANI/1.3" -"fastp - 0.20.0","data-handling","conda","Epigenetics","Cmdline only","https://github.com/OpenGene/fastp","An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...) ","/path/to/fastp/0.20.0" -"FastQC - 0.11.5","quality-control","conda","Transcriptomics","Galaxy and cmdline","http://www.bioinformatics.babraham.ac.uk/projects/fastqc/","A quality control tool for high throughput sequence data","/path/to/fastqc/0.11.5" -"FastQC - 0.11.6","quality-control","conda","Other","Galaxy and cmdline","http://www.bioinformatics.babraham.ac.uk/projects/fastqc/","A quality control tool for high throughput sequence data","/path/to/fastqc/0.11.6" -"FastQC - 0.11.8","quality-control","conda","Epigenetics","Galaxy and cmdline","http://www.bioinformatics.babraham.ac.uk/projects/fastqc/","A quality control tool for high throughput sequence data","/path/to/fastqc/0.11.8" -"fastsimcoal2 - fsc2603","population-genomics","shell","Metagenomics","Cmdline only","http://cmpg.unibe.ch/software/fastsimcoal2/","Fast sequential Markov coalescent simulation of genomic data under complex evolutionary models","/path/to/fastsimcoal2/fsc2603" -"FASTX-Toolkit - 0.0.14","data-handling","conda","Other","Galaxy and cmdline","http://hannonlab.cshl.edu/fastx_toolkit/","Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing","/path/to/fastxtoolkit/0.0.14" -"faToTwoBit - 357","data-handling","conda","Genomics","Cmdline only","https://bioconda.github.io/recipes/ucsc-fatotwobit/README.html","Convert DNA from fasta to 2bit format","/path/to/ucsc-fatotwobit/357" -"Fiji - 20170530","image-analysis","conda","Genomics","Cmdline only","https://imagej.net/Fiji/Downloads","Image processing package","/path/to/fiji/20170530" -"FImpute - 2.2","genotyping","shell","Epigenetics","Cmdline only","http://www.aps.uoguelph.ca/~msargol/fimpute/","a large scale genotype imputation tool using information from relatives","/path/to/fimpute/2.2" -"FLASh - 1.2.11","data-handling","conda","Genomics","Galaxy and cmdline","http://ccb.jhu.edu/software/FLASH/","Fast Length Adjustment of Short reads","/path/to/flash/1.2.11" -"FlowCraft - 1.4.1","workflows","conda","Metabarcoding","Cmdline only","https://github.com/assemblerflow/flowcraft","FlowCraft: a component-based pipeline composer for omics analysis using Nextflow","/path/to/flowcraft/1.4.1" -"Flye - 2.3.3","genome-assembly","conda","Genomics","Cmdline only","https://github.com/fenderglass/Flye","Fast and accurate de novo assembler for single molecule sequencing reads ","/path/to/flye/2.3.3" -"Flye - 2.5","genome-assembly","conda","Metabarcoding","Cmdline only","https://github.com/fenderglass/Flye","Fast and accurate de novo assembler for single molecule sequencing reads ","/path/to/flye/2.5" -"Flye - 2.6","genome-assembly","conda","Metagenomics","Cmdline only","https://github.com/fenderglass/Flye","Fast and accurate de novo assembler for single molecule sequencing reads ","/path/to/flye/2.6" -"Flye - 2.7","genome-assembly","conda","Other","Cmdline only","https://github.com/fenderglass/Flye","Fast and accurate de novo assembler for single molecule sequencing reads ","/path/to/flye/2.7" -"FMLRC - 1.0.0","read-correction","conda","Metagenomics","Cmdline only","https://github.com/holtjma/fmlrc","Tool for performing hybrid correction of long read sequencing","/path/to/fmlrc/1.0.0" -"freebayes - 1.1.0","variant-calling","conda","Transcriptomics","Galaxy and cmdline","https://github.com/ekg/freebayes","Bayesian genetic variant detector designed to find small polymorphisms","/path/to/freebayes/1.1.0" -"freebayes - 1.3.1","variant-calling","conda","Epigenetics","Galaxy and cmdline","https://github.com/ekg/freebayes","Bayesian genetic variant detector designed to find small polymorphisms","/path/to/freebayes/1.3.1" -"FROGS - 1.4.0","community-profiling","conda","Transcriptomics","Cmdline only","https://github.com/geraldinepascal/FROGS","Workflow designed to produce an OTU count matrix from high depth sequencing amplicon data","/path/to/frogs/1.4.0" -"FROGS - 2.0.0","community-profiling","conda","Genomics","Galaxy and cmdline","https://github.com/geraldinepascal/FROGS","Workflow designed to produce an OTU count matrix from high depth sequencing amplicon data","/path/to/frogs/2.0.0" -"Galaxy sequence utils - 1.1.1","data-handling","conda","Multi-thematic","Galaxy only","https://github.com/galaxyproject/sequence_utils","Galaxy sequence utilities are a set of Python modules for reading, analyzing, and converting sequence formats.","/path/to/galaxy_sequence_utils/1.1.1" -"Galaxy sequence utils - 1.1.2","data-handling","conda","Multi-thematic","Galaxy only","https://github.com/galaxyproject/sequence_utils","Galaxy sequence utilities are a set of Python modules for reading, analyzing, and converting sequence formats.","/path/to/galaxy_sequence_utils/1.1.2" -"GATB Minia assembly pipeline - 1.4.1","sequence-assembly","conda","Metabarcoding","Cmdline only","https://github.com/GATB/gatb-minia-pipeline","de novo assembly pipeline for Illumina data","/path/to/gatb-minia-pipeline/1.4.1" -"GATK - 3.7","variant-calling","conda","Metagenomics","Cmdline only","https://software.broadinstitute.org/gatk/","The Genome Analysis Toolkit for short variant discovery and genotyping","/path/to/gatk/3.7" -"GATK - 4.0.2.1","variant-calling","conda","Epigenetics","Cmdline only","https://software.broadinstitute.org/gatk/","The Genome Analysis Toolkit for short variant discovery and genotyping","/path/to/gatk/4.0.2.1" -"GATK - 4.1.3.0","variant-calling","conda","Multi-thematic","Cmdline only","https://software.broadinstitute.org/gatk/","The Genome Analysis Toolkit for short variant discovery and genotyping","/path/to/gatk/4.1.3.0" -"Gblocks - 0.91b","phylogenetic-tree-construction","conda","Metabarcoding","Galaxy and cmdline","https://bioweb.pasteur.fr/docs/modules/gblocks/0.91b/","Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis","/path/to/gblocks/0.91b" -"genBlast - 1.39","gene-prediction","shell","Genomics","Cmdline only","http://genome.sfu.ca/genblast/index.html","enabling BLAST to identify homologous gene sequences","/path/to/genblast/1.39" -"GeneMark - 4.38","gene-prediction","conda","Epigenetics","Cmdline only","http://exon.gatech.edu/GeneMark/","eukaryotic gene finder that can perform gene prediction without curated training sets","/path/to/genemark-es-et/4.38" -"GenericRepeatFinder - 1.0","repeat-sequence-analysis","conda","Metagenomics","Cmdline only","https://github.com/bioinfolabmu/GenericRepeatFinder","C++ program package for detecting terminal inverted repeats (TIRs), terminal direct repeats (TDRs), interspersed repeats, miniature inverted repeat transposable elements (MITEs), and long terminal repeat (LTR) transposons in genomes","/path/to/genericrepeatfinder/1.0" -"GMCloser - 1.6","scaffold-gap-completion","docker","Multi-thematic","Cmdline only","https://sourceforge.net/projects/gmcloser/","GMcloser fills and closes the gaps present in scaffold assemblies","/path/to/gmcloser/1.6" -"GNU Datamash - 1.1.0","data-handling","conda","Other","Galaxy and cmdline","https://www.gnu.org/software/datamash/","Performs basic numeric,textual and statistical operations on input textual data files","/path/to/datamash/1.1.0" -"gowinda - 1.12","enrichment-analysis","docker","Genomics","Cmdline only","https://sourceforge.net/p/gowinda/wiki/Main/","Analysis of gene set enrichment for Genome Wide Association Studies","/path/to/gowinda/1.12" -"GTDB-Tk - 1.0.2","taxonomic-classification","conda","Metagenomics","Cmdline only","https://github.com/Ecogenomics/GTDBTk#bioconda-installation","Toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes","/path/to/gtdbtk/1.0.2" -"guppy - 3.4.4","base-calling","shell","Multi-thematic","Cmdline only","https://nanoporetech.com/","real-time basecalling for Oxford Nanopore Technologies sequencing platforms","/path/to/guppy/3.4.4" -"hapflk - 1.3.0","genotyping","conda","Metagenomics","Cmdline only","https://forge-dga.jouy.inra.fr/projects/hapflk","hapFLK and FLK tests for the detection of selection signatures based on multiple population genotyping data","/path/to/hapflk/1.3.0" -"Haploclique - 1.3.1","haplotype-reconstruction","conda","Epigenetics","Cmdline only","https://github.com/cbg-ethz/haploclique","A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data","/path/to/haploclique/1.3.1" -"HaploConduct - 0.2.1","genome-assembly","conda","Other","Cmdline only","https://github.com/haploconduct/haploconduct","Haplotype-aware genome assembly toolkit ","/path/to/haploconduct/0.2.1" -"HASLR - 0.8a1","genome-assembly","conda","Epigenetics","Cmdline only","https://github.com/vpc-ccg/haslr","A fast tool for hybrid genome assembly of long and short reads ","/path/to/haslr/0.8a1" -"HatCUT2 - 2","genome-assembly","conda","Metabarcoding","Cmdline only","https://github.com/vibansal/HapCUT2/blob/master/README.md","Robust and accurate haplotype assembly for diverse sequencing technologies","/path/to/hapcut/2" -"HHsuite - 3.0-beta.3","sequence-similarity-search","shell","Metabarcoding","Cmdline only","https://github.com/soedinglab/hh-suite/tree/v3.0-beta.3","sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs)","/path/to/hhsuite/3.0-beta.3" -"HISAT2 - 2.0.5","read-mapping","conda","Transcriptomics","Cmdline only","https://ccb.jhu.edu/software/hisat2/index.shtml","Graph-based alignment of next generation sequencing reads to a population of genomes","/path/to/hisat2/2.0.5" -"HISAT2 - 2.1.0","read-mapping","conda","Metagenomics","Galaxy and cmdline","https://ccb.jhu.edu/software/hisat2/index.shtml","Graph-based alignment of next generation sequencing reads to a population of genomes","/path/to/hisat2/2.1.0" -"HMMER - 3.2.1","sequence-similarity-search","conda","Metabarcoding","Cmdline only","http://hmmer.org/documentation.html","biosequence analysis using profile hidden Markov models","/path/to/hmmer/3.2.1" -"HPG-Methyl - 3.2.5","read-mapping","conda","Metagenomics","Cmdline only","https://github.com/grev-uv/hpg-methyl","ultrafast and highly sensitive Next-Generation Sequencing (NGS) read mapper and methylation context extractor","/path/to/hpgmethyl/3.2.5" -"HTSeq-count - 0.6.1","rna-seq-quantification","conda","Genomics","Galaxy and cmdline","http://htseq.readthedocs.io/","Counts for each gene how many reads map to it","/path/to/htseq-count/0.6.1" -"HTSeq-count - 0.9.1","rna-seq-quantification","conda","Transcriptomics","Galaxy and cmdline","http://htseq.readthedocs.io/","Counts for each gene how many reads map to it","/path/to/htseq-count/0.9.1" -"HTStream - 1.2.0","data-handling","conda","Transcriptomics","Cmdline only","https://github.com/ibest/HTStream","Fast, streaming QA/QC for High Throughput Sequencing data","/path/to/htstream/1.2.0" -"HyPhy - 2.3.14","phylogenetic-tree-construction","conda","Transcriptomics","Cmdline only","http://hyphy.org/","Hypothesis Testing using Phylogenies","/path/to/hyphy/2.3.14" -"IDBA - 1.1.3","sequence-assembly","conda","Transcriptomics","Cmdline only","https://github.com/loneknightpy/idba","Iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data","/path/to/idba/1.1.3" -"IGV - 2.5.3","sequence-visualisation","shell","Other","Cmdline only","http://software.broadinstitute.org/software/igv/book/export/html/6","Integrative Genomics Viewer (IGV)","/path/to/igv/2.5.3" -"Illumina_utils - 2.3","data-handling","conda","Other","Cmdline only","https://github.com/merenlab/illumina-utils","a small library and a bunch of clients to perform various operations on FASTQ files","/path/to/illumina-utils/2.3" -"instaGRAAL - 0.1.2","genome-assembly,scaffolding","shell","Multi-thematic","Cmdline only","https://github.com/koszullab/instaGRAAL","Large genome reassembly based on Hi-C data","/path/to/instaGRAAL/0.1.2" -"InterProScan - 5.28-67.0","sequence-annotation","shell","Multi-thematic","Cmdline only","http://www.ebi.ac.uk/interpro/about.html","the software package that allows sequences to be scanned against InterPro's signatures","/path/to/interproscan/5.28-67.0" -"IQ-TREE - 1.5.5.1","phylogenetic-tree-construction","conda","Metabarcoding","Galaxy and cmdline","http://www.iqtree.org/","Stochastic algorithm to infer phylogenetic trees by maximum likelihood.","/path/to/iqtree/1.5.5" -"IQ-TREE - 1.6.7","phylogenetic-tree-construction","conda","Metabarcoding","Cmdline only","http://www.iqtree.org/","Stochastic algorithm to infer phylogenetic trees by maximum likelihood.","/path/to/iqtree/1.6.7" -"JBrowse - 1.12.3","genome-visualisation","conda","Metabarcoding","Cmdline only","https://jbrowse.org/","Genome browser","/path/to/jbrowse/1.12.3" -"jcvi - 0.9.14","genome-assembly,scaffolding","conda","Metagenomics","Cmdline only","https://github.com/tanghaibao/jcvi","Python utility libraries on genome assembly, annotation and comparative genomics ","/path/to/jcvi/0.9.14" -"Jellyfish - 2.2.6","k-mer-counting","conda","Multi-thematic","Cmdline only","http://www.genome.umd.edu/jellyfish.html","counting of k-mers in DNA","/path/to/jellyfish/2.2.6" -"jModelTest2 - 2.1.10","phylogenetic-tree-construction","shell","Genomics","Cmdline only","https://github.com/ddarriba/jmodeltest2","Tool to carry out statistical selection of best-fit models of nucleotide substitution","/path/to/jmodeltest2/2.1.10" -"Kaiju - 1.7.1","taxonomic-classification","conda","Metabarcoding","Cmdline only","https://github.com/bioinformatics-centre/kaiju/blob/master/README.md","Fast and sensitive taxonomic classification for metagenomics","/path/to/kaiju/1.7.1" -"Kaiju - 1.7.3","taxonomic-classification","conda","Metagenomics","Cmdline only","https://github.com/bioinformatics-centre/kaiju/blob/master/README.md","Fast and sensitive taxonomic classification for metagenomics","/path/to/kaiju/1.7.3" -"Kalign - 2.04","multiple-sequence-alignment","shell","Transcriptomics","Cmdline only","http://msa.cgb.ki.se/cgi-bin/msa.cgi","A fast and accurate multiple sequence alignment algorithm","/path/to/kalign/2.04" -"KING - 2.8.1","genotyping","shell","Genomics","Cmdline only","http://people.virginia.edu/~wc9c/KING/","Relationship inference in genome-wide association studies","/path/to/king/2.1.8" -"KisSplice - 2.4.0-p1","transcriptome-assembly","conda","Multi-thematic","Cmdline only","http://kissplice.prabi.fr/","A local transcriptome assembler for SNPs, indels and AS events","/path/to/kissplice/2.4.0p1" -"KMC - 3.1.2rc1","k-mer-counting","conda","Transcriptomics","Cmdline only","https://github.com/refresh-bio/KMC","Fast and frugal disk based k-mer counter ","/path/to/kmc/3.1.2rc1" -"KmerGenie - 1.7016","k-mer-counting","conda","Epigenetics","Cmdline only","http://kmergenie.bx.psu.edu/","estimates the best k-mer length for genome de novo assembly.","/path/to/kmergenie/1.7016" -"KrakenUniq - 0.5.8","taxonomic-classification","conda","Metagenomics","Cmdline only","https://github.com/fbreitwieser/krakenuniq/blob/master/README.md","Confident and fast metagenomics classification using unique k-mer counts","/path/to/krakenuniq/0.5.8" -"Krona - 2.7","visualisation","conda","Other","Galaxy and cmdline","https://sourceforge.net/p/krona/home/krona/","Hierarchical data browser","/path/to/krona/2.7" -"LEfSe - 1.0.8","community-profiling","conda","Metagenomics","Galaxy and cmdline","https://bitbucket.org/biobakery/biobakery/wiki/lefse","Find biomarkers between 2 or more groups using relative abundances","/path/to/lefse/1.0.8" -"Lep-MAP3 - 0.2","linkage-analysis","shell","Epigenetics","Cmdline only","https://sourceforge.net/p/lep-map3/wiki/Home/","a linkage map construction software suite","/path/to/lep-map3/0.2" -"LINKS - 1.8.6","scaffolding","shell","Multi-thematic","Cmdline only","http://www.bcgsc.ca/platform/bioinfo/software/links","Long Interval Nucleotide K-mer Scaffolder","/path/to/links/1.8.6" -"lulu - 0.1","sequence-clustering","conda","Multi-thematic","Cmdline only","https://github.com/tobiasgf/lulu","A r-package for distribution based post clustering curation of amplicon data","/path/to/lulu/0.1" -"MACS - 2.1.1.20160309","chip-seq","conda","Epigenetics","Galaxy and cmdline","https://github.com/taoliu/MACS/","study genome-wide protein-DNA interactions","/path/to/macs2/2.1.1.20160309" -"MACSE - 2.01","multiple-sequence-alignment","conda","Metabarcoding","Cmdline only","https://bioweb.supagro.inra.fr/macse/","Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons","/path/to/macse/2.01" -"MAFFT - 7.245","multiple-sequence-alignment","conda","Epigenetics","Galaxy and cmdline","https://mafft.cbrc.jp/alignment/software/","Multiple alignment program for amino acid or nucleotide sequences","/path/to/mafft/7.245" -"MAFFT - 7.310","multiple-sequence-alignment","conda","Genomics","Galaxy and cmdline","https://mafft.cbrc.jp/alignment/software/","Multiple alignment program for amino acid or nucleotide sequences","/path/to/mafft/7.310" -"marginPhase - 1.0.0","haplotype-reconstruction","singularity","Transcriptomics","Cmdline only","https://github.com/benedictpaten/marginPhase","MarginPhase is a program for simultaneous haplotyping and genotyping","/path/to/marginPhase/1.0.0" -"Mauve - 2.4","genome-alignment","conda","Metabarcoding","Cmdline only","http://darlinglab.org/mauve/mauve.html","Multiple genome alignment","/path/to/mauve/2.4" -"MCScanX - 2019-09-17","synteny","conda","Metagenomics","Cmdline only","http://chibba.pgml.uga.edu/mcscan2/","Multiple Collinearity Scan toolkit","/path/to/mcscanx/2019-09-17" -"Medaka - 0.11.4","sequencing-error-detection","conda","Other","Cmdline only","https://github.com/nanoporetech/medaka","Sequence correction provided by ONT Research ","/path/to/medaka/0.11.4" -"MEGAHIT - 1.1.1","genome-assembly","conda","Other","Cmdline only","https://github.com/voutcn/megahit","Assembler for large and complex metagenomics NGS reads","/path/to/megahit/1.2.9" -"Metabat2 - 2.12.1","read-binning","conda","Other","Cmdline only","https://bitbucket.org/berkeleylab/metabat/src/master/","workflow framework","/path/to/metabat/2.12.1" -"MethPipe - 3.4.3","methylation-analysis","shell","Metagenomics","Cmdline only","http://smithlabresearch.org/software/methpipe/","Analyzing bisulfite sequencing data (WGBS and RRBS)","/path/to/methpipe/3.4.3" -"MethylExtract - 1.9.1","methylation-analysis","docker","Other","Cmdline only","http://bioinfo2.ugr.es/MethylExtract/","Methylation maps and SNV calling from whole genome bisulfite sequencing data","/path/to/methylextract/1.9.1" -"methylKit - 0.99.2","whole-genome-methylation-analysis","conda","Genomics","Galaxy and cmdline","https://bioconductor.org/packages/3.8/bioc/html/methylKit.html","DNA methylation analysis from high-throughput bisulfite sequencing results","/path/to/bioconductor-methylkit/0.99.2" -"MIGRATE-N - 0.11.5","population-genomics","shell","Other","Cmdline only","http://popgen.sc.fsu.edu/Migrate/Migrate-n.html","Estimation of population sizes and gene flow using the coalescent","/path/to/migrate-n/3.6.11" -"miniasm - 0.2_r168","genome-assembly","conda","Metagenomics","Cmdline only","https://github.com/lh3/miniasm","Ultrafast de novo assembly for long noisy reads (though having no consensus step) ","/path/to/miniasm/0.2_r168" -"minimap2 - 2.16","read-mapping","conda","Transcriptomics","Cmdline only","https://lh3.github.io/minimap2","A versatile pairwise aligner for genomic and spliced nucleotide sequences","/path/to/minimap2/2.16" -"minimap2 - 2.17","read-mapping","conda","Metagenomics","Cmdline only","https://lh3.github.io/minimap2","A versatile pairwise aligner for genomic and spliced nucleotide sequences","/path/to/minimap2/2.17" -"minimap2 - 2.9","read-mapping","conda","Metagenomics","Cmdline only","https://lh3.github.io/minimap2","A versatile pairwise aligner for genomic and spliced nucleotide sequences","/path/to/minimap2/2.9" -"MIRA - 4.9.6","genome-assembly","conda","Transcriptomics","Cmdline only","https://sourceforge.net/p/mira-assembler/wiki/Home/","whole genome shotgun and EST sequence assembler for Sanger, 454, Illumina, IonTorrent data and PacBio","/path/to/mira/4.9.6" -"MLST-Check - 2.1.1","multilocus-sequence-typing","docker","Metagenomics","Cmdline only","https://github.com/sanger-pathogens/mlst_check","Multilocus sequence typing by blast using the schemes from PubMLST","/path/to/mlst-check/2.1.1" -"MMseqs2 - 9-d36de","sequence-clustering","conda","Genomics","Cmdline only","https://github.com/soedinglab/MMseqs2/wiki","ultra fast and sensitive search and clustering suite","/path/to/mmseqs2/9-d36de" -"MOSAIK - 2.2.26","read-mapping","conda","Metagenomics","Galaxy and cmdline","https://github.com/wanpinglee/MOSAIK","Mapping second and third-generation sequencing reads to a reference genome","/path/to/mosaik/2.2.26" -"mosdepth - 0.2.7","read-depth-analysis","conda","Multi-thematic","Cmdline only","https://github.com/brentp/mosdepth","Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing ","/path/to/mosdepth/0.2.7" -"mothur - 1.38.1.1","community-profiling","conda","Metabarcoding","Cmdline only","https://www.mothur.org/","Analyzing 16S rRNA gene sequences","/path/to/mothur/1.38.1.1" -"mothur - 1.39.5","community-profiling","conda","Metabarcoding","Cmdline only","https://www.mothur.org/","Analyzing 16S rRNA gene sequences","/path/to/mothur/1.39.5" -"mothur - 1.42.1","community-profiling","conda","Epigenetics","Galaxy and cmdline","https://www.mothur.org/","Analyzing 16S rRNA gene sequences","/path/to/mothur/1.42.1" -"MrBayes - 3.2.6","phylogenetic-tree-construction","conda","Other","Galaxy and cmdline","http://mrbayes.sourceforge.net/","Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models","/path/to/mrbayes/3.2.6" -"MrBayes - 3.2.7","phylogenetic-tree-construction","conda","Metabarcoding","Galaxy and cmdline","http://mrbayes.sourceforge.net/","Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models","/path/to/mrbayes-mpi/3.2.7" -"MultiQC - 1.2","quality-control","conda","Multi-thematic","Cmdline only","http://multiqc.info/","Aggregate results from bioinformatics analyses across many samples into a single report","/path/to/multiqc/1.2" -"MultiQC - 1.5","quality-control","conda","Metabarcoding","Cmdline only","http://multiqc.info/","Aggregate results from bioinformatics analyses across many samples into a single report","/path/to/multiqc/1.5" -"MultiQC - 1.8","quality-control","conda","Metabarcoding","Cmdline only","http://multiqc.info/","Aggregate results from bioinformatics analyses across many samples into a single report","/path/to/multiqc/1.8" -"MUMmer - 3.23","genome-alignment","conda","Transcriptomics","Cmdline only","https://github.com/mummer4/mummer","Versatil alignment tool for DNA and protein sequences","/path/to/mummer/3.23" -"MUMmer - 4.0.0beta2","genome-alignment","conda","Transcriptomics","Cmdline only","https://github.com/mummer4/mummer","Versatil alignment tool for DNA and protein sequences","/path/to/mummer/4.0.0beta2" -"muscle - 3.8","multiple-sequence-alignment","conda","Genomics","Cmdline only","https://www.ebi.ac.uk/Tools/msa/muscle/","MUltiple Sequence Comparison by Log- Expectation","/path/to/muscle/3.8" -"nano - 2.2.6","editing","shell","Transcriptomics","Cmdline only","https://www.nano-editor.org/dist/v3/nano.html","Simple text editor","/path/to/nano/2.2.6" -"NanoFilt - 2.6.0","data-handling","conda","Other","Cmdline only","https://github.com/wdecoster/nanofilt","Streaming script for filtering a fastq file based on a minimum length, minimum quality cut-off, minimum and maximum average GC","/path/to/nanofilt/2.6.0" -"NanoPlot - 1.28.0","quality-control","conda","Transcriptomics","Cmdline only","https://github.com/wdecoster/NanoPlot","Creating many relevant plots derived from reads (fastq), alignments (bam) and albacore/guppy summary files","/path/to/nanoplot/1.28.2" -"NCBI Blast+ - 2.2.31","sequence-similarity-search","conda","Transcriptomics","Cmdline only","https://blast.ncbi.nlm.nih.gov/Blast.cgi","Basic Local Alignment Search Tool","/path/to/blast/2.2.31" -"NCBI Blast+ - 2.6.0","sequence-similarity-search","conda","Transcriptomics","Galaxy and cmdline","https://blast.ncbi.nlm.nih.gov/Blast.cgi","Basic Local Alignment Search Tool","/path/to/blast/2.6.0" -"NCBI Blast+ - 2.9.0","sequence-similarity-search","conda","Epigenetics","Cmdline only","https://blast.ncbi.nlm.nih.gov/Blast.cgi","Basic Local Alignment Search Tool","/path/to/blast/2.9.0" -"NCBI Blast-legacy - 2.2.26","sequence-similarity-search","shell","Metabarcoding","Cmdline only","https://blast.ncbi.nlm.nih.gov/Blast.cgi","Basic Local Alignment Search Tool","/path/to/blast-legacy/2.2.26" -"Nextflow - 18.10.1","workflows","conda","Other","Cmdline only","https://www.nextflow.io/docs/latest/basic.html","workflow framework","/path/to/nextflow/18.10.1" -"Nextflow - 19.07.0","workflows","conda","Transcriptomics","Cmdline only","https://www.nextflow.io/docs/latest/basic.html","workflow framework","/path/to/nextflow/19.07.0" -"Nextflow - 20.01.0","workflows","conda","Multi-thematic","Cmdline only","https://www.nextflow.io/docs/latest/basic.html","workflow framework","/path/to/nextflow/20.01.0" -"NGSUtils - 0.5.9","data-handling","conda","Multi-thematic","Cmdline only","http://ngsutils.org/","Suite of software tools for working with next-generation sequencing datasets","/path/to/ngsutils/0.5.9" -"npScarf - 2019.09","scaffolding","conda","Genomics","Cmdline only","https://github.com/mdcao/npScarf","Scaffolding and Completing Assemblies in Real-time Fashion","/path/to/npscarf/2019.09" -"OAU - 1.2","sequence-similarity","shell","Transcriptomics","Cmdline only","https://www.ezbiocloud.net/tools/orthoaniu","Average nucleotide identity (ANI) calculator, which uses the improved ANI algorithm (OrthoANI) with USEARCH","/path/to/oau/1.2" -"Octopus - 0.6.3b","variant-calling,haplotype-mapping","conda","Metabarcoding","Cmdline only","https://github.com/luntergroup/octopus","Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework","/path/to/octopus/0.6.3b" -"Oligotyping - 2.1","community-profiling","conda","Multi-thematic","Cmdline only","http://merenlab.org/software/oligotyping/","Investigate diversity within their OTUs at a precise level by utilizing subtle variations among 16S Ribosomal RNA gene sequences","/path/to/oligotyping/2.1" -"OPERA-LG - 2.0.6","scaffolding","conda","Metabarcoding","Cmdline only","https://sourceforge.net/projects/operasf/","A program for scaffolding of large, repeat-rich eukaryotic genomes","/path/to/opera-lg/2.0.6" -"P_RNA_scaffolder - 2019.09","scaffolding","shell","Metabarcoding","Cmdline only","https://github.com/CAFS-bioinformatics/P_RNA_scaffolder","Use paired-end transcriptome reads to scaffold genomes","/path/to/p_rna_scaffolder/2019.09" -"PAL_FINDER - 0.02.04","variant-calling","conda","Transcriptomics","Cmdline only","https://sourceforge.net/projects/palfinder/","Finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads, and designs PCR primers to amplify these repeat loci in an automated fashion","/path/to/pal_finder/0.02.04" -"pb-assembly/Falcon - 0.0.8-0","genome-assembly","conda","Metabarcoding","Cmdline only","https://github.com/PacificBiosciences/pb-assembly","FALCON is a diploid-aware assembler which follows the hierarchical genome assembly process (HGAP) and is optimized for large genome assembly though microbial genomes can also be assembled","/path/to/pb-assembly/0.0.8-0" -"PCAdapt - 3.0.4","gene-prediction","conda","Epigenetics","Cmdline only","http://membres-timc.imag.fr/Michael.Blum/PCAdapt.html","Genome scan for detecting genes involved in local adaptation","/path/to/pcadapt/3.0.4" -"PEAR - 0.9.6","read-preprocessing","conda","Metabarcoding","Cmdline only"," https://sco.h-its.org/exelixis/web/software/pear/doc.html","An ultrafast, memory-efficient and highly accurate pair-end read merger","/path/to/pear/0.9.6" -"PfamScan - 1.6","sequence-similarity-search","conda","Other","Cmdline only","https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/PfamScan+Help+and+Documentation","Search a sequence against a library of Pfam hidden Markov models (HMM)","/path/to/pfam-scan/1.6" -"PHYLIP - 3.696","phylogenetic-tree-construction","conda","Transcriptomics","Galaxy and cmdline","http://evolution.genetics.washington.edu/phylip.html","Inferring parsimony phylogenies","/path/to/phylip/3.696" -"phyloseq - 1.14.2","community-profiling","conda","Transcriptomics","Cmdline only","https://joey711.github.io/phyloseq/","Analyze microbiome census data using R","/path/to/bioconductor-phyloseq/1.14.2" -"PhyML - 3.1","phylogenetic-tree-construction","shell","Epigenetics","Cmdline only","http://www.atgc-montpellier.fr/phyml/","Estimate Maximum-Likelihook Phylogenies","/path/to/phyml/3.1" -"PhyML - 3.3.2","phylogenetic-tree-construction","conda","Multi-thematic","Galaxy and cmdline","http://www.atgc-montpellier.fr/phyml/","Estimate Maximum-Likelihook Phylogenies","/path/to/phyml/3.3.2" -"Picard - 2.21.1","data-handling","conda","Transcriptomics","Cmdline only","https://github.com/broadinstitute/picard","A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats","/path/to/picard/2.21.1" -"PICRUSt - 1.1.0","functional-predictions","conda","Metabarcoding","Cmdline only","http://picrust.github.io/picrust/","Predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.","/path/to/picrust/1.1.0" -"Pilon - 1.23","sequencing-error-detection","conda","Epigenetics","Cmdline only","https://github.com/broadinstitute/pilon/","Pilon is an automated genome assembly improvement and variant detection tool ","/path/to/Pilon/1.23" -"PLASS - 2.7.35","sequence-assembly","conda","Epigenetics","Cmdline only","https://github.com/soedinglab/plass","Protein-Level ASSembler ","/path/to/plass/2.7.35" -"PLAST - 2.3.2","sequence-similarity-search","shell","Epigenetics","Galaxy and cmdline","https://plast.inria.fr/user-guide/","High Performance Parallel Local Alignment Search Tool","/path/to/plast/2.3.2" -"PLAST - 2.3.3","sequence-similarity-search","shell","Transcriptomics","Galaxy and cmdline","https://plast.inria.fr/user-guide/","High Performance Parallel Local Alignment Search Tool","/path/to/plast/2.3.3" -"Platanus - 1.2.4","genome-assembly","shell","Genomics","Cmdline only","http://platanus.bio.titech.ac.jp/","Genome assembler","/path/to/platanus/1.2.4" -"Platanus - 2.0.2","genome-assembly","conda","Other","Cmdline only","http://platanus.bio.titech.ac.jp/platanus2","Platanus-allee is a de novo haplotype assembler","/path/to/platanus/2.0.2" -"Platypus variant - 0.8.1.2","variant-calling","conda","Other","Cmdline only","https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data","A Haplotype-Based Variant Caller For Next Generation Sequence Data","/path/to/platypus-variant/0.8.1.2" -"PLINK - 1.07","genome-wide-association-study","shell","Metabarcoding","Galaxy and cmdline","http://zzz.bwh.harvard.edu/plink/","whole genome association analysis toolset","/path/to/plink/1.07" -"PLINK - 1.9","genome-wide-association-study","shell","Metabarcoding","Galaxy and cmdline","http://zzz.bwh.harvard.edu/plink/","whole genome association analysis toolset","/path/to/plink/1.9" -"PointFinder - 2018-05-23","variant-calling","conda","Transcriptomics","Cmdline only","https://bitbucket.org/genomicepidemiology/pointfinder","detects chromosomal mutations predictive of drug resistance based on WGS data","/path/to/pointfinder/2018-05-23" -"PoPoolation2 - 1201","variant-classification","docker","Metabarcoding","Cmdline only","https://sourceforge.net/p/popoolation2/wiki/Main/","Compare allele frequencies for SNPs between two or more populations and to identify significant differences","/path/to/popoolation2/1201" -"Prinseq - 0.20.4","sequence-trimming","conda","Epigenetics","Cmdline only","http://prinseq.sourceforge.net/manual.html","filter, reformat and trim NGS data","/path/to/prinseq/0.20.4" -"ProbCons - 1.12","multiple-sequence-alignment","shell","Metagenomics","Cmdline only","http://probcons.stanford.edu/download.html","Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences","/path/to/probcons/1.12" -"Prokka - 1.12","gene-prediction","conda","Epigenetics","Galaxy and cmdline","http://www.vicbioinformatics.com/software.prokka.shtml","Annotation of prokaryotic genomes","/path/to/prokka/1.12" -"Prokka - 1.13","gene-prediction","conda","Other","Cmdline only","http://www.vicbioinformatics.com/software.prokka.shtml","Annotation of prokaryotic genomes","/path/to/prokka/1.13" -"Prokka - 1.13.7","gene-prediction","conda","Multi-thematic","Galaxy and cmdline","http://www.vicbioinformatics.com/software.prokka.shtml","Annotation of prokaryotic genomes","/path/to/prokka/1.13.7" -"Prokka - 1.14.5","gene-prediction","conda","Other","Galaxy and cmdline","http://www.vicbioinformatics.com/software.prokka.shtml","Annotation of prokaryotic genomes","/path/to/prokka/1.14.5" -"Prokka - 1.14.6","gene-prediction","conda","Epigenetics","Galaxy and cmdline","http://www.vicbioinformatics.com/software.prokka.shtml","Annotation of prokaryotic genomes","/path/to/prokka/1.14.6" -"pycoQC - 2.5.0.19","quality-control","conda","Metagenomics","Galaxy and cmdline","https://github.com/a-slide/pycoQC","pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)","/path/to/pycoqc/2.5.0.19" -"pyScaf - 0.12a","scaffolding","conda","Epigenetics","Cmdline only","https://github.com/lpryszcz/pyScaf","Orders contigs from genome assemblies","/path/to/pyscaf/0.12a" -"QIIME 2 - 2.0.0","community-profiling","conda","Metabarcoding","Cmdline only","http://qiime2.org/","Pipeline for performing microbiome analysis from raw DNA sequencing data","/path/to/qiime/2.0.0" -"QIIME 2 - 2019.04","community-profiling","conda","Epigenetics","Cmdline only","https://qiime2.org/","Pipeline for performing microbiome analysis from raw DNA sequencing data","/path/to/qiime/2019.04" -"QIIME 2 - 2019.07","community-profiling","conda","Transcriptomics","Cmdline only","https://qiime2.org/","Pipeline for performing microbiome analysis from raw DNA sequencing data","/path/to/qiime/2019.07" -"QIIME 2 - 2019.10","community-profiling","conda","Multi-thematic","Cmdline only","https://qiime2.org/","Pipeline for performing microbiome analysis from raw DNA sequencing data","/path/to/qiime/2019.10" -"QIIME 2 - 2020.02","community-profiling","conda","Transcriptomics","Cmdline only","https://qiime2.org/","Pipeline for performing microbiome analysis from raw DNA sequencing data","/path/to/qiime/2020.02" -"QIIME - 1.9.1","community-profiling","conda","Transcriptomics","Cmdline only","http://qiime.org/","Pipeline for performing microbiome analysis from raw DNA sequencing data","/path/to/qiime/1.9.1" -"QuasiRecomb - 1.2","recombination-detection","conda","Metagenomics","Cmdline only","https://github.com/cbg-ethz/QuasiRecomb","Probabilistic inference of viral quasispecies subject to recombination (viral haplotype reconstruction)","/path/to/quasirecomb/1.2" -"QUAST - 4.5","sequence-assembly-validation","conda","Other","Cmdline only","http://bioinf.spbau.ru/quast","Evaluates genome assemblies","/path/to/quast/4.5" -"QUAST - 4.6.3","sequence-assembly-validation","conda","Epigenetics","Cmdline only","http://bioinf.spbau.ru/quast","Evaluates genome assemblies","/path/to/quast/4.6.3" -"QUAST - 5.0.0","sequence-assembly-validation","conda","Metabarcoding","Cmdline only","http://bioinf.spbau.ru/quast","Evaluates genome assemblies","/path/to/quast/5.0.0" -"QUAST - 5.0.2","sequence-assembly-validation","conda","Metagenomics","Galaxy and cmdline","http://bioinf.spbau.ru/quast","Evaluates genome assemblies","/path/to/quast/5.0.2" -"r - 3.5.1","statistics-and-probability,visualisation","conda","Epigenetics","Cmdline only","https://www.r-project.org/","R base","/path/to/R/3.5.1" -"r - 3.6.1","statistics-and-probability,visualisation","conda","Other","Cmdline only","https://www.r-project.org/","R base","/path/to/R/3.6.1" -"r-metabarcoding-toolbox - 1.0","community-profiling","conda","Metagenomics","Cmdline only","https://w3z.ifremer.fr/bioinfo/Cmdline-Datarmor/Ressources-disponibles/Les-toolboxes-creees-a-facon/R-Metabarcoding-toolbox","Homemade toolbox with common tools used in R for metabacording analysis","/path/to/r-metabarcoding-toolbox/1.0" -"Racon - 1.4.10","sequencing-error-detection","conda","Metabarcoding","Cmdline only","https://github.com/lbcb-sci/racon","Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads ","/path/to/racon/1.4.10" -"Raven - 0.0.7","genome-assembly","conda","Metagenomics","Cmdline only","https://github.com/lbcb-sci/raven","De novo genome assembler for long uncorrected reads","/path/to/raven/0.0.7" -"RAxML - 8.2.12","phylogenetic-tree-construction","conda","Metabarcoding","Cmdline only","https://sco.h-its.org/exelixis/web/software/raxml/index.html","Randomized Axelerated Maximum Likelihood.","/path/to/raxml/8.2.12" -"Rcorrector - 1.0.3","read-correction","conda","Metabarcoding","Galaxy and cmdline","https://github.com/mourisl/Rcorrector","kmer-based error correction method for RNA-seq data","/path/to/rcorrector/1.0.3" -"Rcorrector - 1.0.4","read-correction","conda","Metabarcoding","Galaxy and cmdline","https://github.com/mourisl/Rcorrector","kmer-based error correction method for RNA-seq data","/path/to/rcorrector/1.0.4" -"remoVecSec - 0.02","sequence-contamination-filtering","conda","Multi-thematic","Cmdline only","https://github.com/htafer/remoVecSec","Module and script to remove contamination in assembled genomes before submission to ncbi ","/path/to/remoVecSec/0.0.2" -"REPdenovo - 0.0.1","repeat-sequence-analysis","conda","Metagenomics","Cmdline only","https://github.com/simoncchu/REPdenovo","constructing repeats directly from sequence reads","/path/to/repdenovo/0.0.1" -"RepeatModeler - 1.0.11","repeat-sequence-analysis","conda","Metagenomics","Cmdline only","https://github.com/rmhubley/RepeatModeler","De-Novo Repeat Discovery Tool","/path/to/repeatmodeler/1.0.11" -"RepeatModeler - 2.0.1","repeat-sequence-analysis","conda","Metagenomics","Cmdline only","https://github.com/rmhubley/RepeatModeler","De-Novo Repeat Discovery Tool","/path/to/repeatmodeler/2.0.1" -"RpARK - 1.3.0","repeat-sequence-analysis","conda","Multi-thematic","Cmdline only","https://github.com/PhKoch/RepARK","wrapper script for constructing a repeat library from sequencing reads","/path/to/repark/1.3.0" -"RStudio - 1.1.456","statistics-and-probability,visualisation","conda","Epigenetics","Cmdline only","https://rstudio.com/","Tool for statistics","/path/to/rstudio/1.1.456" -"Salmon - 2.7.0d","rna-seq-quantification","conda","Metabarcoding","Galaxy and cmdline","https://combine-lab.github.io/salmon/","quantifying the expression of transcripts using RNA-seq data","/path/to/salmon/0.13.1" -"sambamba - 0.6.6","data-handling","conda","Transcriptomics","Cmdline only","https://github.com/biod/sambamba","parallel robust and fast tool for working with SAM and BAM files","/path/to/sambamba/0.6.6" -"SAMtools - 1.10","data-handling","conda","Metabarcoding","Cmdline only","http://samtools.sourceforge.net/","Provides various utilities for manipulating alignments in the SAM format","/path/to/samtools/1.10" -"SAMtools - 1.4.1","data-handling","conda","Transcriptomics","Galaxy and cmdline","http://samtools.sourceforge.net/","Provides various utilities for manipulating alignments in the SAM format","/path/to/samtools/1.4.1" -"SAMtools - 1.6","data-handling","conda","Other","Cmdline only","http://samtools.sourceforge.net/","Provides various utilities for manipulating alignments in the SAM format","/path/to/samtools/1.6" -"SAMtools - 1.9","data-handling","conda","Metabarcoding","Galaxy and cmdline","http://samtools.sourceforge.net/","Provides various utilities for manipulating alignments in the SAM format","/path/to/samtools/1.9" -"SarTools - 1.3.2","statistical-calculation","conda","Epigenetics","Galaxy and cmdline","https://github.com/PF2-pasteur-fr/SARTools","A tool for statistical analysis of RNA-Seq","/path/to/sartools/1.3.2" -"Scrappie - 1.4.2","base-calling","conda","Genomics","Cmdline only","https://github.com/nanoporetech/scrappie","Technology demonstrator for the Oxford Nanopore Research Algorithms group","/path/to/scrappie/1.4.2" -"seqkit - 0.9.1","data-handling","conda","Metagenomics","Cmdline only","https://bioinf.shenwei.me/seqkit","Tool to manipulate fastq files","/path/to/seqkit/0.9.1" -"SeqTk - 1.2","data-handling","conda","Other","Galaxy and cmdline","https://github.com/lh3/seqtk","A fast and lightweight tool for processing sequences in the FASTA or FASTQ format","/path/to/seqtk/1.2" -"SeqTk - 1.3","data-handling","conda","Genomics","Cmdline only","https://github.com/lh3/seqtk","A fast and lightweight tool for processing sequences in the FASTA or FASTQ format","/path/to/seqtk/1.3" -"SGA - 0.10.15","genome-assembly","conda","Other","Cmdline only","https://github.com/jts/sga","De novo sequence assembler using string graphs","/path/to/sga/0.10.15" -"shasta - 0.4.0","genome-assembly","shell","Genomics","Cmdline only","https://github.com/chanzuckerberg/shasta","De novo assembly from Oxford Nanopore reads.","/path/to/shasta/0.4.0" -"ShoRAH - 1.1.0","variant-calling,haplotype-mapping","conda","Transcriptomics","Cmdline only","https://github.com/cbg-ethz/shorah","Short Reads Assembly into Haplotypes","/path/to/shorah/1.1.0" -"shovill - 1.0.9","genome-assembly","conda","Epigenetics","Galaxy and cmdline","https://github.com/tseemann/shovill","Microbial assembly pipeline for Illumina paired-end reads","/path/to/shovill/1.0.9" -"signalP - 4.1","sequence-motif-recognition","shell","Other","Cmdline only","http://www.cbs.dtu.dk/services/SignalP/","predicts the presence and location of signal peptide cleavage sites in amino acid sequences ","/path/to/signalp/4.1" -"Simka - 1.4","community-profiling","shell","Multi-thematic","Cmdline only","https://github.com/GATB/simka","De novo comparative metagenomics tool","/path/to/simka/1.4" -"SMRT Tools - 5.1.0","workflows","shell","Transcriptomics","Cmdline only","http://programs.pacificbiosciences.com/l/1652/2018-03-20/3wrpm7/1652/190674/SMRT_Tools_Reference_Guide__v5.1.0_.pdf","Suite available for analysis of DNA sequencing data from Pacific Biosciences’ SMRT technology","/path/to/smrt-tools/5.1.0" -"Smudgeplot - 0.2.0","quality-control","conda","Genomics","Cmdline only","https://github.com/KamilSJaron/smudgeplot","Inference of ploidy and heterozygosity structure using whole genome sequencing data","/path/to/smudgeplot/0.2.0" -"Smudgeplot - 0.2.3","quality-control","conda","Metabarcoding","Cmdline only","https://github.com/KamilSJaron/smudgeplot","Inference of ploidy and heterozygosity structure using whole genome sequencing data","/path/to/smudgeplot/0.2.3" -"Snakemake - 5.4.0","workflows","conda","Transcriptomics","Cmdline only","https://snakemake.readthedocs.io/en/stable/","workflow framework","/path/to/snakemake/5.4.0" -"Sniffles - 1.0.7","variant-calling","conda","Transcriptomics","Cmdline only","https://github.com/fritzsedlazeck/Sniffles","structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)","/path/to/sniffles/1.0.7" -"Snippy - 4.1.0","variant-calling","conda","Metagenomics","Cmdline only","https://github.com/tseemann/snippy","Rapid haploid variant calling and core SNP phylogeny","/path/to/snippy/4.1.0" -"Snippy - 4.4.0","variant-calling","conda","Metagenomics","Galaxy and cmdline","https://github.com/tseemann/snippy","Rapid haploid variant calling and core SNP phylogeny","/path/to/snippy/4.4.0" -"Snpeff - 4.3","variant-classification","conda","Transcriptomics","Galaxy and cmdline","http://snpeff.sourceforge.net/SnpEff.html","A genetic variant annotation and functional effect prediction toolbox","/path/to/snpeff/4.3" -"SOAPdenovo - 2.40","genome-assembly","conda","Multi-thematic","Cmdline only","http://soap.genomics.org.cn/soapdenovo.html#inst2","short-read assembly method that can build a de novo draft assembly for the human-sized genomes","/path/to/soapdenovo/2.40" -"SortMeRNA - 2.1b","read-preprocessing","conda","Metabarcoding","Cmdline only","https://github.com/biocore/sortmerna","next-generation sequence filtering and alignment tool","/path/to/sortmerna/2.1b" -"SourceTracker - 1.0.1","community-profiling","shell","Other","Cmdline only","https://github.com/danknights/sourcetracker/","Bayesian approach to estimating the proportion of a novel community that comes from a set of source environments","/path/to/sourcetracker/1.0.1" -"SourceTracker - 2.0.1","community-profiling","conda","Genomics","Cmdline only","https://github.com/biota/sourcetracker2/","Bayesian approach to estimating the proportion of a novel community that comes from a set of source environments","/path/to/sourcetracker/2.0.1" -"sourmash - 2.0.0","sequence-similarity","conda","Genomics","Cmdline only","https://github.com/dib-lab/sourmash","Compute MinHash signatures for nucleotide (DNA/RNA) and protein sequences","/path/to/sourmash/2.0.0" -"Spades - 3.10.1","sequence-assembly","conda","Genomics","Cmdline only","http://cab.spbu.ru/software/spades/","An assembly toolkit containing various assembly pipelines","/path/to/spades/3.10.1" -"Spades - 3.11.0","sequence-assembly","conda","Multi-thematic","Galaxy and cmdline","http://cab.spbu.ru/software/spades/","An assembly toolkit containing various assembly pipelines","/path/to/spades/3.11.0" -"Spades - 3.12.0","sequence-assembly","conda","Metagenomics","Galaxy and cmdline","http://cab.spbu.ru/software/spades/","An assembly toolkit containing various assembly pipelines","/path/to/spades/3.12.0" -"Spades - 3.13.0","sequence-assembly","conda","Epigenetics","Cmdline only","http://cab.spbu.ru/software/spades/","An assembly toolkit containing various assembly pipelines","/path/to/spades/3.13.0" -"Spades - 3.14.0","sequence-assembly","conda","Transcriptomics","Cmdline only","http://cab.spbu.ru/software/spades/","An assembly toolkit containing various assembly pipelines","/path/to/spades/3.14.0" -"SRA Toolkit - 2.10.1","data-handling","conda","Epigenetics","Cmdline only","https://github.com/ncbi/sra-tools","The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives","/path/to/sra-tools/2.10.1" -"SSpace-long read - 1.1","scaffolding","conda","Metagenomics","Cmdline only","https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-211","A program for scaffolding pre-assembled contigs using long reads","/path/to/sspace-longread/1.1" -"SSpace-Standard - 3.0","scaffolding","conda","Genomics","Cmdline only","https://www.baseclear.com/services/bioinformatics/basetools/sspace-standard/","stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data","/path/to/sspace-standard/3.0" -"Stacks - 1.46","population-genomics","conda","Transcriptomics","Cmdline only","http://catchenlab.life.illinois.edu/stacks/","An analysis tool set for population genomics","/path/to/stacks/1.46" -"Stacks - 2.0Beta8","population-genomics","conda","Multi-thematic","Cmdline only","http://catchenlab.life.illinois.edu/stacks/","An analysis tool set for population genomics","/path/to/stacks/2.0Beta8" -"Stacks - 2.0Beta9","population-genomics","conda","Epigenetics","Cmdline only","http://catchenlab.life.illinois.edu/stacks/","An analysis tool set for population genomics","/path/to/stacks/2.0Beta9" -"Star - 2.5.3a","read-mapping","conda","Genomics","Cmdline only","https://github.com/alexdobin/STAR#manual","A ultrafast universal RNA-seq aligner","/path/to/star/2.5.3a" -"Star - 2.7.0d","read-mapping","conda","Metagenomics","Galaxy and cmdline","https://github.com/alexdobin/STAR#manual","A ultrafast universal RNA-seq aligner","/path/to/star/2.7.0d" -"T-Coffee - 11.0.8","multiple-sequence-alignment","conda","Other","Galaxy and cmdline","http://www.tcoffee.org/","A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments","/path/to/t_coffee/11.0.8" -"TMHMM - 2.0","sequence-motif-recognition","shell","Metagenomics","Cmdline only","http://www.cbs.dtu.dk/services/TMHMM/","prediction of transmembrane helices in proteins","/path/to/tmhmm/2.0" -"Tophat2 - 2.1.1","read-mapping","conda","Transcriptomics","Galaxy and cmdline","https://ccb.jhu.edu/software/tophat/manual.shtml","A fast splice junction mapper for RNA-Seq reads","/path/to/tophat2/2.1.1" -"TransDecoder - 3.0.1","gene-prediction,coding-region-prediction","conda","Multi-thematic","Galaxy and cmdline","https://github.com/TransDecoder/TransDecoder/wiki","identifies candidate coding regions within transcript sequences","/path/to/transdecoder/3.0.1" -"transrate - 1.0.3","sequence-assembly-validation","conda","Multi-thematic","Cmdline only","http://hibberdlab.com/transrate/index.html","de-novo transcriptome assembly quality analysis","/path/to/transrate/1.0.3" -"Trimal - 1.4.1","sequence-trimming","conda","Other","Galaxy and cmdline","http://trimal.cgenomics.org/","A tool for automated alignment trimming in large-scale phylogenetic analyses","/path/to/trimal/1.4.1" -"Trimgalore - 0.4.1","quality-control,sequence-trimming","conda","Multi-thematic","Cmdline only","http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf","A tool to automate quality and adapter trimming as well as quality control","/path/to/trim-galore/0.4.1" -"Trimgalore - 0.6.2","quality-control,sequence-trimming","conda","Transcriptomics","Cmdline only","https://github.com/FelixKrueger/TrimGalore","A tool to automate quality and adapter trimming as well as quality control","/path/to/trim-galore/0.6.4" -"Trimgalore - 0.6.3","quality-control,sequence-trimming","conda","Transcriptomics","Cmdline only","https://github.com/FelixKrueger/TrimGalore","A tool to automate quality and adapter trimming as well as quality control","/path/to/trim-galore/0.6.3" -"Trimmomatic - 0.36","sequence-trimming","conda","Epigenetics","Galaxy and cmdline","http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf","A flexible trimmer for Illumina sequence data","/path/to/trimmomatic/0.36" -"Trinity - 2.4.0","transcriptome-assembly","conda","Other","Cmdline only","https://github.com/trinityrnaseq/trinityrnaseq/wiki","De novo assembly of RNA-Seq data","/path/to/trinity/2.4.0" -"Trinity - 2.5.1","transcriptome-assembly","conda","Transcriptomics","Cmdline only","https://github.com/trinityrnaseq/trinityrnaseq/wiki","De novo assembly of RNA-Seq data","/path/to/trinity/2.5.1" -"Trinity - 2.8.4","transcriptome-assembly","conda","Epigenetics","Galaxy and cmdline","https://github.com/trinityrnaseq/trinityrnaseq/wiki","De novo assembly of RNA-Seq data","/path/to/trinity/2.8.4" -"Trinity - 2.8.5","transcriptome-assembly","conda","Metabarcoding","Galaxy and cmdline","https://github.com/trinityrnaseq/trinityrnaseq/wiki","De novo assembly of RNA-Seq data","/path/to/trinity/2.8.5" -"Trinotate - 3.1.1","sequence-annotation","conda","Transcriptomics","Galaxy and cmdline","https://github.com/Trinotate/Trinotate","Annotate transcripts generated by Trinity","/path/to/trinotate/3.1.1" -"UGENE - 1.32.0","sequence-visualisation,workflows","shell","Metabarcoding","Cmdline only","http://ugene.net/documentation.html","free open-source cross-platform bioinformatics software","/path/to/ugene/1.32.0" -"Unicycler - 0.4.8","genome-assembly","conda","Epigenetics","Galaxy and cmdline","https://github.com/rrwick/Unicycler","Assembly pipeline for bacterial genomes","/path/to/unicycler/0.4.8" -"VarScan - 4.2.3","variant-calling","conda","Metagenomics","Galaxy and cmdline","http://dkoboldt.github.io/varscan/","variant detection in massively parallel sequencing data","/path/to/varscan/2.4.3" -"vcflib - 1.0.0_rc1","data-handling","conda","Multi-thematic","Cmdline only","https://github.com/vcflib/vcflib","provides methods to manipulate and interpret sequence variation as it can be described by VCF","/path/to/vcflib/1.0.0_rc1" -"VCFTools - 0.1.14","data-handling","conda","Multi-thematic","Cmdline only","https://vcftools.github.io/index.html","Program package designed for working with VCF files","/path/to/vcftools/0.1.14" -"VCFTools - 0.1.16","data-handling","conda","Genomics","Galaxy and cmdline","https://vcftools.github.io/index.html","Program package designed for working with VCF files","/path/to/vcftools/0.1.16" -"Velvet - 1.2.10","genome-assembly","conda","Metagenomics","Galaxy and cmdline","https://www.ebi.ac.uk/~zerbino/velvet","Sequence assembler for very short reads","/path/to/velvet/1.2.10" -"vsearch - 2.11.1","sequence-clustering","shell","Multi-thematic","Cmdline only","https://github.com/torognes/vsearch","vectorized search, the open-source alternative to usearch","/path/to/vsearch/2.11.1" -"vt - 2015.11.10","variant-calling","conda","Genomics","Cmdline only","https://github.com/atks/vt","tool set for short variant discovery in genetic sequence data","/path/to/vt/2015.11.10" -"w2rap-contigger - 2019-07-11","sequence-assembly","shell","Metabarcoding","Cmdline only","http://bioinfologics.github.io/the-w2rap-contigger/","An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes","/path/to/w2rap-contigger/20190711" -"wengan - 0.1","genome-assembly","shell","Transcriptomics","Cmdline only","https://github.com/adigenova/wengan","An accurate and ultra-fast hybrid genome assembler","/path/to/wengan/0.1" -"WhatsHap - 0.18","genome-assembly","conda","Metabarcoding","Cmdline only","https://whatshap.readthedocs.io/en/latest/","WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly","/path/to/whatshap/0.18" -"WHdenovo - 14012020","genome-assembly","conda","Multi-thematic","Cmdline only","https://github.com/shilpagarg/WHdenovo","A cost-effective approach to diploid assembly for single samples and trios","/path/to/WHdenovo/14012020" -"wtdbg2/Readbean - 2.5","genome-assembly","conda","Metagenomics","Cmdline only","https://github.com/ruanjue/wtdbg2","A fuzzy Bruijn graph approach to long noisy reads assembly","/path/to/wtdbg2/2.5" -"yacrd - 0.6.0","quality-control","conda","Metagenomics","Cmdline only","https://github.com/natir/yacrd","Yet Another Chimeric Read Detector","/path/to/yacrd/0.6.0" -"zUMIs - 2.7.0","rna-seq-analysis,workflows","conda","Other","Cmdline only","https://github.com/sdparekh/zUMIs","A fast and flexible pipeline to process RNA sequencing data with UMIs","/path/to/zumis/2.7.0" +Name,Version,Operation,Topic,Doc,Description,Environment,Galaxy,Workflow +"ABACAS","1.3.1-conda","scaffold-gap-completion","Sequence assembly","http://abacas.sourceforge.net/","Algorithm Based Automatic Contiguation of Assembled Sequences.","conda","false","false" +"abricate","0.9.8-conda","gene-prediction","Functional genomics","https://github.com/tseemann/abricate","Mass screening of contigs for antibiotic resistance genes","conda","true","false" +"ADMIXTURE","1.3.0-shell","genetic-variation-analysis","Population genetics","https://dalexander.github.io/admixture/index.html","Fast ancestry estimation","shell","false","false" +"AGAT","0.8.0-conda","data-handling","Bioinformatics","https://github.com/NBISweden/AGAT","Another Gff Analysis Toolkit (AGAT)","conda","false","false" +"AlienTrimmer","0.4.2-conda","sequence-trimming","Bioinformatics","https://bioweb.pasteur.fr/packages/pack@AlienTrimmer@0.4.0","A software that allows detecting and removing contaminant sequences in both ends of NGSread sequences FASTA/FASTQ formated.","conda","false","false" +"Alvis","1.2-singularity","visualisation,quality-control,taxonomic-partitioning","Data visualisation","https://alvis.readthedocs.io/en/latest/index.html","no description provided by authors","singularity","false","false" +"andi","0.13-singularity","sequence-distance-matrix-generation","Phylogenetics","https://github.com/EvolBioInf/andi","Program for estimating the evolutionary distance between closely related genomes.","singularity","false","false" +"ANGSD","0.933-conda,0.931-conda,0.923-conda","genotyping","Population genetics","http://www.popgen.dk/angsd/index.php/ANGSD","Analysis of next generation Sequencing Data","conda","false","false" +"antiSMASH","6.0.1-conda,5.1.2-conda","sequence-clustering,gene-prediction","Gene and protein families","https://antismash.secondarymetabolites.org/#!/start","Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes","conda","false","false" +"anvi'o","7dev-conda,7-conda,6.2-conda,6-conda,5.1.0-conda,4-conda","visualisation,workflows","Metagenomics","http://merenlab.org/software/anvio/","advanced analysis and visualization platform for omics data","conda","false","false" +"ARB","6.0.6-conda","visualisation,phylogenetic-analysis","Phylogeny","http://www.arb-home.de/documentation.html","Silva visualization tool","conda","false","false" +"ARCS","1.0.5-conda","genome-assembly,scaffolding","Sequence assembly","https://github.com/bcgsc/arcs/tree/v1.0.5","Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data.","conda","false","false" +"Aria2","1.36.0-conda","data-handling","Bioinformatics","http://aria2.github.io/","The lightweight multi-protocol & multi-source command-line download utility.","conda","false","false" +"ARIBA","2.14.6-conda","sequence-clustering,gene-prediction","Gene and protein families","https://github.com/sanger-pathogens/ariba","Antimicrobial Resistance Identification By Assembly","conda","false","false" +"ARLSUMSTAT","3.5.2-shell","statistics-and-probability","Population genetics","http://cmpg.unibe.ch/software/arlequin35/man/arlsumstat_readme.txt","modified version of Arlequin for computing summary statistics","shell","false","false" +"ARTIC","1.2.1-conda","sequence-alignment","Metagenomics","https://artic.readthedocs.io/en/latest/","Pipeline and set of accompanying tools for working with viral nanopore sequencing data.","conda","false","false" +"ibm-aspera-connect","3.10.0-singularity","data-handling","Bioinformatics","https://www.ibm.com/support/knowledgecenter/SSXMX3_3.10/connect_user_linux/guide.html","Enable high-speed FASP transfers","singularity","false","false" +"AUGUSTUS","3.3-conda","gene-prediction","Functional genomics","http://augustus.gobics.de/","gene prediction program for eukaryotes","conda","false","false" +"AWS-Cli","v2-shell","data-handling","Bioinformatics","https://docs.aws.amazon.com/cli/latest/userguide/cli-chap-welcome.html","Amazon Web Service Client","shell","false","false" +"Bam","0.5.1-conda","data-handling","Bioinformatics","https://matricks.github.io/bam/bam.html","Bam is a build system with the focus on being having fast build times and flexiable build scripts","conda","false","false" +"bam2fastq","1.1.0-conda","data-handling","Bioinformatics","https://github.com/jts/bam2fastq","Simple convertor from bam to FASTQ ","conda","false","false" +"bam2fastx","1.3.1-conda,1.3.0-conda","data-handling","Bioinformatics","https://github.com/PacificBiosciences/bam2fastx","Conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data","conda","false","false" +"BamTools","2.5.1-conda","data-handling","Bioinformatics","https://github.com/pezmaster31/bamtools","Both a programmer's API and an end-user's toolkit for handling BAM files","conda","false","false" +"bamUtil","1.0.14-conda","data-handling","Bioinformatics","https://github.com/statgen/bamUtil","repository that contains several programs that perform operations on SAM/BAM files","conda","false","false" +"Bandage","0.8.1-conda","sequence-visualisation","Sequence assembly","https://github.com/rrwick/Bandage","a Bioinformatics Application for Navigating De novo Assembly Graphs Easily","conda","false","false" +"barrnap","0.9-conda","gene-prediction","Sequence analysis","https://github.com/tseemann/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).","conda","true","false" +"BaseSpace CLI","1.0.0-shell","data-handling","Bioinformatics","https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview","scripting and programmatic access to Illumina BaseSpace Sequence Hub","shell","false","false" +"cutadapt","38.57-conda,1.18-conda","sequence-trimming","Bioinformatics","https://cutadapt.readthedocs.io/en/stable/","Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads","conda","true","false" +"bbtools","34.62-conda","data-handling","Bioinformatics","https://jgi.doe.gov/data-and-tools/bbtools/","BBMap short read aligner, and other bioinformatic tools (reads filter, reads merge, sequences converter) ","conda","false","false" +"BCFtools","1.4.1-conda,1.13-conda,1.10.2-conda","data-handling","Bioinformatics","https://samtools.github.io/bcftools/bcftools.html","Utilities for variant calling and manipulating VCFs and BCFs.","conda","true","false" +"Beagle","4.0_06Jun17-conda","genotyping","Genotype and phenotype","https://faculty.washington.edu/browning/beagle/b4_0.html","Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection","conda","false","false" +"beast2","2.6.3-conda","phylogenetic-tree-reconstruction","Phylogeny","http://www.beast2.org","Bayesian phylogenetic analysis of molecular sequences.","conda","false","false" +"BEDOPS","2.4.38-conda","workflows","Bioinformatics","https://github.com/bedops/bedops","high-performance genomic feature operations","conda","false","false" +"bedtools","2.30.0-conda,2.27.1-conda,2.26.0-conda","data-handling","Bioinformatics","http://bedtools.readthedocs.io/en/latest/","Toolset for genome arithmetic","conda","false","false" +"BeeDeeM-Tools","2.1.0-shell,2.0.1-shell,2.0.0-shell","data-handling","Biological databases","https://gitlab.ifremer.fr/bioinfo/BeeDeeM-Tools/blob/master/documentation/tutorial.md","sequence-based data analysis pipeline tools","shell","false","false" +"BeeDeeM","4.7.0-singularity","database-management","Biological databases","https://github.com/pgdurand/BeeDeeM/wiki","a Bioinformatics Databank Manager System","singularity","false","false" +"Bioawk","1.0-conda","data-handling","Bioinformatics","https://github.com/lh3/bioawk","Extension to Brian Kernighan's awk, adding the support of several common biological data formats","conda","false","false" +"bioconductor-chromstaR","1.8.1-conda","chip-seq","Epigenetics","https://bioconductor.org/packages/3.8/bioc/html/chromstaR.html","Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data","conda","false","false" +"bioconductor-dada2","1.8.0-conda,1.6.0-conda","genetic-variation-analysis","Metagenomics","https://bioconductor.org/packages/release/bioc/html/dada2.html","Accurate, high-resolution sample inference from amplicon sequencing data","conda","false","false" +"DESeq2","1.20.0-conda,1.14.1-conda","differential-gene-expression-analysis","Transcriptomics","https://bioconductor.org/packages/release/bioc/html/DESeq2.html","Differential gene expression analysis based on the negative binomial distribution","conda","true","false" +"methylKit","0.99.2-conda","whole-genome-methylation-analysis","Epigenetics","https://bioconductor.org/packages/3.8/bioc/html/methylKit.html","DNA methylation analysis from high-throughput bisulfite sequencing results","conda","true","false" +"phyloseq","1.14.2-conda","community-profiling","Metagenomics","https://joey711.github.io/phyloseq/","Analyze microbiome census data using R","conda","false","false" +"bioconductor-tximport ","1.16.0-conda","data-handling","Transcriptomics","https://bioconductor.org/packages/3.11/bioc/html/tximport.html","Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages","conda","true","false" +"biom-format","2.1.6-conda","conversion","Bioinformatics","http://biom-format.org/documentation/biom_conversion.html","Converting between file formats","conda","true","false" +"Bioperl","1.7.2-conda","data-handling","Bioinformatics","https://bioperl.org","Perl tools for comutational molecular biology","conda","false","false" +"Biopython","latest-conda,1.78-conda,1.70-conda","data-handling","Bioinformatics","http://biopython.org/DIST/docs/tutorial/Tutorial.html","Python tools for comutational molecular biology","conda","false","false" +"Bismark","0.20.0-conda,0.19-conda,0.17-conda","bisulfite-mapping","Epigenetics","http://www.bioinformatics.babraham.ac.uk/projects/bismark/","A tool to map bisulfite converted sequence reads and determine cytosine methylation states","conda","false","false" +"BisSNP","0.82.2-docker","methylation-calling","Epigenetics","http://people.csail.mit.edu/dnaase/bissnp2011/","Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller","docker","false","false" +"BLASR","5.3.3-conda","read-mapping","Mapping","https://github.com/PacificBiosciences/blasr","BLASR: The PacBio long read aligner ","conda","false","false" +"NCBI Blast-legacy","2.2.26-shell","sequence-similarity-search","Biological databases","https://blast.ncbi.nlm.nih.gov/Blast.cgi","Basic Local Alignment Search Tool","shell","false","false" +"NCBI Blast+","2.9.0-conda,2.6.0-conda,2.2.31-conda,2.12.0-conda","sequence-similarity-search","Biological databases","https://blast.ncbi.nlm.nih.gov/Blast.cgi","Basic Local Alignment Search Tool","conda","false","false" +"BlastViewer","5.2.0-shell","sequence-similarity-search,visualisation","Biological databases","https://github.com/pgdurand/BlastViewer/wiki","A graphical workbench to analyse BLAST result files.","shell","false","false" +"BlobToolKit","1.3.6-singularity","visualisation,quality-control,taxonomic-partitioning","Data visualisation","https://blobtoolkit.genomehubs.org","a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies","singularity","false","false" +"blobtools","2.6.3-conda,1.1-conda","visualisation,quality-control,taxonomic-partitioning","Data visualisation","https://github.com/DRL/blobtools","A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets ","conda","false","false" +"blupf90","unknown-shell","analysis","Population genetics","http://nce.ads.uga.edu/html/projects/programs/","BLUPF90 family of programs is a collection of software in Fortran 90/95 for mixed model computations in animal breeding.","shell","false","false" +"bowtie2","2.4.5-conda,2.4.4-conda,2.4.1-conda,2.3.5-conda,2.3.4.3-conda,2.3.4.1-conda,2.3.0-conda","read-mapping","Mapping","http://bowtie-bio.sourceforge.net/bowtie2/index.shtml","Aligning sequencing reads to long reference sequences","conda","true","false" +"BRAKER2","2.1.6-singularity,2.1.5-singularity","gene-prediction","Functional genomics","https://github.com/Gaius-Augustus/BRAKER","BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes ","singularity","false","false" +"BS-SNPer","master-docker","methylation-calling","Epigenetics","https://github.com/hellbelly/BS-Snper","Exploration of SNP sites from BS-Seq data","docker","false","false" +"bsmap","2.90-conda","bisulfite-mapping","Epigenetics","https://code.google.com/archive/p/bsmap/","short reads mapping software for bisulfite sequencing reads","conda","true","false" +"bsmapz","1.1.3-conda,1.1.1-conda","bisulfite-mapping","Epigenetics","https://github.com/zyndagj/BSMAPz","short reads mapping software for bisulfite sequencing reads","conda","true","false" +"BUSCO","5.2.2-conda,5.1.1-conda,5.0.0-conda,4.1.4-conda,4.1.3-conda,4.0.6-conda,4.0.4-conda,4.0.0-conda,3.0.2-conda","sequence-assembly-validation","Sequence assembly","http://busco.ezlab.org/","Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs","conda","false","false" +"bwa-mem2","2.2.1-conda,2.1-conda","read-mapping","Mapping","https://github.com/bwa-mem2/bwa-mem2","Burrow-Wheeler Aligner for short-read alignment.","conda","false","false" +"BWA","0.7.17-conda,0.7.15-conda","read-mapping","Mapping","http://bio-bwa.sourceforge.net/","Mapping low-divergent sequences against a large reference genome","conda","true","false" +"bwa-meth","0.2.3-conda","bisulfite-mapping","Epigenetics","https://github.com/brentp/bwa-meth","Fast and accurante alignment of BS-Seq reads.","conda","false","false" +"Canu","2.2-conda,2.1.1-conda,2.0-conda,1.9-conda,1.7-conda,1.6-conda","genome-assembly","Sequence assembly","http://canu.readthedocs.io","A single molecule sequence assembler for genomes large and small","conda","false","false" +"cap3","10.2011-conda","genome-assembly","Sequence assembly,Sequence analysis","http://biosrv.cab.unina.it/webcap3/","Web-based contig assembly.","conda","false","false" +"cd-hit","4.8.1-shell","sequence-clustering","Bioinformatics","http://weizhongli-lab.org/cd-hit/","clustering and comparing protein or nucleotide sequences","shell","true","false" +"Centrifuge","1.0.3-conda","taxonomic-classification","Metagenomics","https://github.com/infphilo/centrifuge","Classifier for metagenomic sequences","conda","false","false" +"CheckM-genome","1.1.3-conda","sequence-assembly-validation","Sequence assembly","https://ecogenomics.github.io/CheckM/","GAPPadder is designed for closing gaps on the draft genomes with paired-end reads or mate-paired reads.","conda","false","false" +"CheckV","0.5.1-conda","sequence-assembly-validation","Metagenomics","https://bitbucket.org/berkeleylab/checkv/src/master/","A fully automated command-line pipeline for assessing the quality of metagenome-assembled viral genomes","conda","false","false" +"CIAlign","1.0.15-conda","sequence-alignement-analysis","Sequence analysis","https://github.com/KatyBrown/CIAlign/","A command line tool which performs various functions to clean and analyse a multiple sequence alignment (MSA)","conda","false","false" +"circos","0.69.6-conda","data-visualisation","Data visualisation","http://circos.ca","package for visualizing data and information. It visualizes data in a circular layout","conda","false","false" +"Clair","2.1.1-conda","variant-calling","Comparative genomics","https://github.com/HKU-BAL/Clair","deep neural network based variant caller","conda","false","false" +"Clair3","0.1-r4.2-conda,0.1-conda","variant-calling","Comparative genomics","https://github.com/HKU-BAL/Clair3","deep neural network based variant caller","conda","false","false" +"Clustal Omega","1.2.3-conda","multiple-sequence-alignment","Phylogeny","http://www.clustal.org/omega/","Multiple sequence alignement","conda","true","false" +"Clustal W","2.1-conda","multiple-sequence-alignment","Phylogeny","http://www.clustal.org/omega/","Multiple alignment of nucleic acid and protein sequences ","conda","true","false" +"CNVkit","0.9.5-conda","variant-calling","Comparative genomics","http://cnvkit.readthedocs.org","Copy number variant detection from targeted DNA sequencing","conda","false","false" +"concoct","1.1.0-singularity,1.0.0-conda","read-binning","Metagenomics","https://github.com/BinPro/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.","singularity,conda","false","false" +"CONSENT","2.2.2-shell,1.2-shell","read-correction","Sequence assembly","https://github.com/morispi/CONSENT","self-correction method for long reads","shell","false","false" +"CpGIScan","master-shell","sequence-similarity-search","Biological databases","https://github.com/jianzuoyi/CpGIScan","an ultrafast tool for CpG islands identification from genome sequences","shell","false","false" +"CRISP","0.7-conda","variant-calling","Epigenetics","https://bansal-lab.github.io/software/crisp.html","Detect SNPs and short indels from high-throughput sequencing of pooled DNA samples","conda","false","false" +"Cufflinks","2.2.1-conda","transcriptome-assembly,gene-expression-analysis","Transcriptomics","http://cole-trapnell-lab.github.io/cufflinks/","Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples","conda","false","false" +"CulebrONT","1.6-Snakemake,1.4-Snakemake","genome-assembly","Sequence assembly,Workflows","https://culebront-pipeline.readthedocs.io/en/latest/","scalable, modular and traceable Snakemake pipeline, able to launch multiple assembly tools in parallel, giving you the possibility of circularise, polish, and correct assemblies, checking quality","Snakemake","false","false" +"cupcake","28.0.0-conda","data-handling","Transcriptomics","https://github.com/Magdoll/cDNA_Cupcake","Miscellaneous collection of Python and R scripts for processing Iso-Seq data","conda","false","false" +"cutadapt","2.8-conda,1.18-conda,1.16-conda,1.13-conda","sequence-trimming","Bioinformatics","https://cutadapt.readthedocs.io/en/stable/","Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads","conda","true","false" +"dada2","1.10-conda","community-profiling","Metagenomics","https://benjjneb.github.io/dada2/index.html","Fast and accurate sample inference from amplicon data with single-nucleotide resolution","conda","false","false" +"DAS_Tool","1.1.3-conda","read-binning","Metagenomics","https://github.com/cmks/DAS_Tool","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.","conda","false","false" +"GNU Datamash","1.1.0-conda","data-handling","Bioinformatics","https://www.gnu.org/software/datamash/","Performs basic numeric,textual and statistical operations on input textual data files","conda","true","false" +"dbCAN2","2.0.6-shell","sequence-annotation","Functional genomics","https://github.com/linnabrown/run_dbcan","Tools to handle CAZyme annotation","shell","false","false" +"DBG2OLC","20180222-conda,20160205-conda","genome-assembly","Sequence assembly","https://github.com/yechengxi/DBG2OLC","Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies","conda","false","false" +"dbgwas","0.5.3-singularity","genetic-variation-analysis","GWAS study","https://gitlab.com/leoisl/dbgwas","DBGWAS is a tool for quick and efficient bacterial GWAS","singularity","false","false" +"Deepbinner","0.2.0-conda","demultiplexing","Bioinformatics","https://github.com/rrwick/Deepbinner","Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads.","conda","false","false" +"DeepMod","0.1.3-conda","methylation-analysis","Epigenetics","https://github.com/WGLab/DeepMod","a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications.","conda","false","false" +"DeepMP","master-conda","methylation-analysis","Epigenetics","https://github.com/pepebonet/DeepMP#Installation","Convolutional neural network (CNN)-based model that takes information from Nanopore signals and basecalling errors to detect whether a read is methylated or not.","conda","false","false" +"DeepSignal-plant","0.1.4-conda","methylation-analysis","Epigenetics","https://github.com/PengNi/deepsignal-plant","A deep-learning method for detecting methylation state from Oxford Nanopore sequencing reads of plants.","conda","false","false" +"DeepSignal2","0.1.0-conda","methylation-analysis","Epigenetics","https://github.com/PengNi/deepsignal2","A deep-learning method for detecting methylation state from Oxford Nanopore sequencing reads.","conda","false","false" +"deepTools","3.4.3-conda","data-handling,visualisation","Bioinformatics","https://deeptools.readthedocs.io/en/develop/","tools for exploring deep sequencing data","conda","false","false" +"DeepVariant","1.1.0-singularity","variant-calling","Comparative genomics","https://github.com/google/deepvariant","DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.","singularity","false","false" +"diamond","2.0.9-singularity,2.0.6-conda,2.0.14-conda,2.0.12-singularity,0.9.24-shell","sequence-similarity-search","Biological databases","https://github.com/bbuchfink/diamond","sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data","singularity,conda,shell","false","false" +"DiscoSNP","2.4.4-conda","variant-calling","Comparative genomics","https://gatb.inria.fr/software/discosnp/","Tool for discovering Single Nucleotide Polymorphism","conda","false","false" +"DRAP","1.91-docker","genome-assembly","Transcriptomics","http://www.sigenae.org/drap/","De novo RNA-seq Assembly Pipeline","docker","false","false" +"dRep","2.2.3-conda","genome-alignment","Metagenomics","https://github.com/MrOlm/drep","dRep is a python program for rapidly comparing large numbers of genomes","conda","false","false" +"Dsuite","master-shell","data-handling","Bioinformatics","https://github.com/millanek/Dsuite","Dsuite ‐ fast D‐statistics and related admixture evidence from VCF files","shell","false","false" +"eCAMI","master-conda","sequence-annotation","Functional genomics","https://github.com/zhanglabNKU/eCAMI","Simultaneous Classification and Motif Identification for enzyme/CAZyme annotation","conda","false","false" +"eggnog-mapper","2.1.0-conda,1.0.3-conda","sequence-annotation","Functional genomics","http://eggnog-mapper.embl.de","Fast genome-wide functional annotation through orthology assignment","conda","false","false" +"Eigensoft","7.2.1-conda","population-structure","Population genetics","https://www.hsph.harvard.edu/alkes-price/software/","Analyze population structure and perform stratification correction","conda","false","false" +"ElConcatenero","current-conda","data-handling","Phylogeny","https://github.com/ODiogoSilva/ElConcatenero","ElConcatenero3 is a python program that converts and concatenates common population genetics and phylogenetics data file types (such as Fasta, Phylip and Nexus)","conda","false","false" +"EMBOSS","6.5.7-conda","data-handling","Bioinformatics","http://emboss.sourceforge.net/","Analysis package specially developed for the needs of the molecular biology","conda","false","false" +"ensembl-vep","105.0-conda","genetic-variation-analysis","Genetic variation","https://github.com/Ensembl/ensembl-vep","VEP (Variant Effect Predictor) predicts the functional effects of genomic variants","conda","false","false" +"evo","current-singularity","data-handling","Bioinformatics","https://github.com/millanek/evo","A loose set of tools for (mainly evolutionary) genomics","singularity","false","false" +"fasta-splitter","0.2.4-conda","data-handling","Bioinformatics","http://kirill-kryukov.com/study/tools/fasta-splitter/","Divides a large FASTA file into a set of smaller, approximately equally sized files","conda","false","false" +"FastANI","1.3-conda","sequence-alignment-similarity","Comparative genomics","https://github.com/ParBLiSS/FastANI","Fast Whole-Genome Similarity (ANI) Estimation ","conda","true","false" +"fastp","0.20.1-conda,0.20.0-conda,0.19.5-conda","data-handling","Bioinformatics","https://github.com/OpenGene/fastp","An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...) ","conda","false","false" +"fastq-pair","1.0-conda","quality-control","Bioinformatics","https://github.com/linsalrob/fastq-pair","Match up paired end fastq files quickly and efficiently","conda","false","false" +"FastQC","0.11.9-conda,0.11.8-conda,0.11.6-conda,0.11.5-conda","quality-control","Bioinformatics","http://www.bioinformatics.babraham.ac.uk/projects/fastqc/","A quality control tool for high throughput sequence data","conda","true","false" +"fastsimcoal2","fsc2603-shell","population-genomics","Population genetics","http://cmpg.unibe.ch/software/fastsimcoal2/","Fast sequential Markov coalescent simulation of genomic data under complex evolutionary models","shell","false","false" +"faststructure","1.0-conda","genetic-variation-analysis","Population genetics","http://rajanil.github.io/fastStructure/","fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.","conda","false","false" +"FASTX-Toolkit","0.0.14-conda","data-handling","Bioinformatics","http://hannonlab.cshl.edu/fastx_toolkit/","Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing","conda","true","false" +"FeGenie","1.1-conda","read-binning","Sequence assembly,Metagenomics","https://github.com/Arkadiy-Garber/FeGenie","HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes","conda","false","false" +"FigTree","1.4.4-conda","phylogenetic-tree-visualisation","Phylogenetics","https://github.com/rambaut/figtree","A graphical viewer of phylogenetic trees","conda","false","false" +"Fiji","20170530-conda","image-analysis","Bioimaging","https://imagej.net/Fiji/Downloads","Image processing package","conda","false","false" +"FImpute","2.2-shell","genotyping","Genotype and phenotype","http://www.aps.uoguelph.ca/~msargol/fimpute/","a large scale genotype imputation tool using information from relatives","shell","false","false" +"FImpute3","2019-09-22019-09-24-shell","genotyping","Genotype and phenotype","http://www.aps.uoguelph.ca/~msargol/fimpute/","a large scale genotype imputation tool using information from relatives","shell","false","false" +"FLASh","1.2.11-conda","data-handling","Bioinformatics","http://ccb.jhu.edu/software/FLASH/","Fast Length Adjustment of Short reads","conda","true","false" +"FlowCraft","1.4.1-conda","workflows","Bioinformatics","https://github.com/assemblerflow/flowcraft","FlowCraft: a component-based pipeline composer for omics analysis using Nextflow","conda","false","false" +"Flye","2.9-conda,2.8.3-conda,2.8.2-conda,2.8.1-conda,2.8-conda,2.7.1-conda,2.7-conda,2.6-conda,2.5-conda,2.3.3-conda","genome-assembly","Sequence assembly","https://github.com/fenderglass/Flye","Fast and accurate de novo assembler for single molecule sequencing reads ","conda","false","false" +"FMLRC","1.0.0-conda","read-correction","Sequence assembly","https://github.com/holtjma/fmlrc","Tool for performing hybrid correction of long read sequencing","conda","false","false" +"FoldX","5.0-conda","protein-folding-analysis","Protein folds and structural domains","http://foldxsuite.crg.eu/documentation#manual","fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes","conda","false","false" +"FragGeneScan","1.31-conda","gene-prediction","Sequence analysis","https://omics.informatics.indiana.edu/FragGeneScan/","An application for finding (fragmented) genes in short reads","conda","false","false" +"freebayes","1.3.5-conda,1.3.2-conda,1.3.1-conda,1.1.0-conda","variant-calling","Comparative genomics","https://github.com/ekg/freebayes","Bayesian genetic variant detector designed to find small polymorphisms","conda","true","false" +"FROGS","3.2.1-conda,2.0.0-conda,1.4.0-conda","community-profiling","Metagenomics","https://github.com/geraldinepascal/FROGS","Workflow designed to produce an OTU count matrix from high depth sequencing amplicon data","conda","false","false" +"Galaxy sequence utils","1.1.2-conda,1.1.1-conda","data-handling","Bioinformatics","https://github.com/galaxyproject/sequence_utils","Galaxy sequence utilities are a set of Python modules for reading, analyzing, and converting sequence formats.","conda","true","false" +"GAPPadder","master-conda","scaffold-gap-completion","Sequence assembly","https://github.com/simoncchu/GAPPadder","GAPPadder is designed for closing gaps on the draft genomes with paired-end reads or mate-paired reads.","conda","false","false" +"gapseq","1.1-conda","metabolic-network-modelling","Genotype and phenotype","https://github.com/jotech/gapseq","Informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models.","conda","false","false" +"GATB Minia assembly pipeline","1.4.1-conda","sequence-assembly","Sequence assembly","https://github.com/GATB/gatb-minia-pipeline","de novo assembly pipeline for Illumina data","conda","false","false" +"GATK","4.2.0.0-conda,4.1.3.0-conda,4.0.2.1-conda,3.7-conda","variant-calling","Comparative genomics","https://software.broadinstitute.org/gatk/","The Genome Analysis Toolkit for short variant discovery and genotyping","conda","false","false" +"Gblocks","0.91b-conda","phylogenetic-tree-construction","Phylogeny","https://bioweb.pasteur.fr/docs/modules/gblocks/0.91b/","Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis","conda","true","false" +"Gemma","0.98.5-shell","genetic-variation-analysis","GWAS study","https://github.com/genetics-statistics/GEMMA","Genome-wide Efficient Mixed Model Association","shell","false","false" +"genBlast","1.39-shell","gene-prediction","Functional genomics","http://genome.sfu.ca/genblast/index.html","enabling BLAST to identify homologous gene sequences","shell","false","false" +"GeneMark","4.38-conda","gene-prediction","Functional genomics","http://exon.gatech.edu/GeneMark/","eukaryotic gene finder that can perform gene prediction without curated training sets","conda","false","false" +"GeneMarkS-T","5.1-conda","gene-prediction","Functional genomics","http://topaz.gatech.edu/GeneMark/","Sets of assembled eukaryotic transcripts can be analyzed by the modified GeneMarkS algorithm (the set should be large enough to permit self-training). A single transcript can be analyzed by a special version of GeneMark.hmm with Heuristic models. A new advanced algorithm GeneMarkS-T was developed recently (manuscript sent to publisher).","conda","false","false" +"GenericRepeatFinder","1.0-conda","repeat-sequence-analysis","Sequence composition, complexity and repeats","https://github.com/bioinfolabmu/GenericRepeatFinder","C++ program package for detecting terminal inverted repeats (TIRs), terminal direct repeats (TDRs), interspersed repeats, miniature inverted repeat transposable elements (MITEs), and long terminal repeat (LTR) transposons in genomes","conda","false","false" +"genomescope2","2.0-conda","sequence-assembly","Sequence assembly","https://github.com/tbenavi1/genomescope2.0","Reference-free profiling of polyploid genomes","conda","false","false" +"GenomeThreader","1.7.3-shell","sequence-feature-detection","Gene structure","http://genomethreader.org/","a software tool to compute gene structure predictions.","shell","false","false" +"genometools","1.6.1-conda","sequence-analysis","Bioinformatics","http://genometools.org/","Free collection of bioinformatics tools for genome informatics.","conda","false","false" +"GetOrganelle","1.7.5.0-conda","genome-assembly","Sequence assembly","https://github.com/Kinggerm/GetOrganelle","A fast and versatile toolkit for accurate de novo assembly of organelle genomes.","conda","false","false" +"gfa1","2faeed2-shell","data-handling","Bioinformatics","https://github.com/lh3/gfa1","A command-line tool as well as a library in C that parses, validates and transforms assembly graphs in a dialect of the GFA1 format","shell","false","false" +"gfatools","0.4-conda","data-handling","Bioinformatics","https://github.com/lh3/gfa1","A command-line tool as well as a library in C that parses, validates and transforms assembly graphs in a dialect of the GFA1 format","conda","false","false" +"gffcompare","0.11.2-conda","sequence-annotation","Sequence analysis","https://ccb.jhu.edu/software/stringtie/gffcompare.shtml","gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files","conda","false","false" +"gffread","0.12.7-conda","sequence-annotation","Sequence analysis","https://github.com/gpertea/gffread","GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more","conda","false","false" +"gfftobed","1.3-shell","data-handling","Bioinformatics","https://github.com/jacobbierstedt/gfftobed","Convert GFF3/GTF to BED","shell","false","false" +"GLnexus","1.2.7-singularity","variant-calling","Comparative genomics","https://github.com/dnanexus-rnd/GLnexus","Scalable gVCF merging and joint variant calling for population sequencing projects.","singularity","false","false" +"gmap","2021.08.25-conda,2020.06.01-conda","genetic-mapping","Mapping","http://research-pub.gene.com/gmap/","Genomic Mapping and Alignment Program for mRNA and EST Sequences.","conda","false","false" +"GMCloser","1.6-docker","scaffold-gap-completion","Sequence assembly","https://sourceforge.net/projects/gmcloser/","GMcloser fills and closes the gaps present in scaffold assemblies","docker","false","false" +"goenrichment","2.0.1-conda","gene-set-enrichment-analysis","Transcriptomics","https://github.com/DanFaria/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. ","conda","true","false" +"google-cloud-sdk","322.0.0-conda","data-handling","Bioinformatics","https://cloud.google.com/sdk/docs","Command-line interface for Google Cloud Platform products and services","conda","false","false" +"gowinda","1.12-docker","enrichment-analysis","Functional genomics","https://sourceforge.net/p/gowinda/wiki/Main/","Analysis of gene set enrichment for Genome Wide Association Studies","docker","false","false" +"GraphBin","1.3-conda,1.1-conda","read-binning","Metagenomics","https://github.com/Vini2/GraphBin","Refined Binning of Metagenomic Contigs using Assembly Graphs","conda","false","false" +"GTDB-Tk","1.5.0-conda,1.4.1-conda,1.1.0-conda,1.0.2-conda","taxonomic-classification","Metagenomics","https://github.com/Ecogenomics/GTDBTk#bioconda-installation","Toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes","conda","false","false" +"guppy","5.0.7-shell,4.5.3-shell,4.4.0-shell,4.2.2-shell,4.0.15-shell,3.6.0-shell,3.4.4-shell,3.3.3-shell","base-calling","Sequence assembly","https://nanoporetech.com/","real-time basecalling for Oxford Nanopore Technologies sequencing platforms","shell","false","false" +"hap.py","v0.3.12-singularity","Oxford Nanopore and PacBio HiFi variant calling","Comparative genomics","https://github.com/kishwarshafin/pepper","Evaluate the variants","singularity","false","false" +"HatCUT2","2-conda","genome-assembly","Sequence assembly","https://github.com/vibansal/HapCUT2/blob/master/README.md","Robust and accurate haplotype assembly for diverse sequencing technologies","conda","false","false" +"hapflk","1.3.0-conda","genotyping","Genotype and phenotype","https://forge-dga.jouy.inra.fr/projects/hapflk","hapFLK and FLK tests for the detection of selection signatures based on multiple population genotyping data","conda","false","false" +"Haploclique","1.3.1-conda","haplotype-reconstruction","Sequence assembly","https://github.com/cbg-ethz/haploclique","A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data","conda","false","false" +"HaploConduct","0.2.1-conda","genome-assembly","Sequence assembly","https://github.com/haploconduct/haploconduct","Haplotype-aware genome assembly toolkit ","conda","false","false" +"Haploflow","1.0-conda","genome-assembly","Sequence assembly","https://github.com/hzi-bifo/Haploflow","a strain-aware viral genome assembler for short read sequence data.","conda","false","false" +"HASLR","0.8a1-conda","genome-assembly","Sequence assembly","https://github.com/vpc-ccg/haslr","A fast tool for hybrid genome assembly of long and short reads ","conda","false","false" +"HHsuite","3.0-beta.3-shell","sequence-similarity-search","Bioinformatics","https://github.com/soedinglab/hh-suite/tree/v3.0-beta.3","sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs)","shell","false","false" +"hifiasm","0.16.1-shell,0.16-shell,0.15.4-shell,0.15.2-shell,0.15-shell,0.14.2-shell,0.14-conda,0.13-conda,0.11-shell","genome-assembly","Sequence assembly","https://github.com/chhylp123/hifiasm","Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads.","shell,conda","false","false" +"HISAT2","2.2.1-conda,2.1.0-conda,2.0.5-conda","read-mapping","Mapping","https://ccb.jhu.edu/software/hisat2/index.shtml","Graph-based alignment of next generation sequencing reads to a population of genomes","conda","false","false" +"HMMER (mpi)","3.3-shell","sequence-similarity-search","Bioinformatics","http://hmmer.org/","Biosequence analysis using profile hidden Markov models","shell","false","false" +"HMMER","3.3.2-conda,3.3-conda,3.2.1-conda","sequence-similarity-search","Bioinformatics","http://hmmer.org/documentation.html","biosequence analysis using profile hidden Markov models","conda","false","false" +"Homopolish","0.3.2-conda","genome-assembly","Sequence assembly","https://github.com/ythuang0522/homopolish","A genome polisher originally developed for Nanopore and subsequently extended for PacBio CLR","conda","false","false" +"HPG-Methyl","3.2.5-conda","read-mapping","Epigenetics","https://github.com/grev-uv/hpg-methyl","ultrafast and highly sensitive Next-Generation Sequencing (NGS) read mapper and methylation context extractor","conda","false","false" +"HTSeq-count","0.9.1-conda,0.6.1-conda,0.13.5-conda","rna-seq-quantification","Transcriptomics","http://htseq.readthedocs.io/","Counts for each gene how many reads map to it","conda","true","false" +"HTStream","1.2.0-conda","data-handling","Bioinformatics","https://github.com/ibest/HTStream","Fast, streaming QA/QC for High Throughput Sequencing data","conda","false","false" +"HyPhy","2.3.14-conda","phylogenetic-tree-construction","Phylogeny","http://hyphy.org/","Hypothesis Testing using Phylogenies","conda","false","false" +"IDBA","1.1.3-conda","sequence-assembly","Sequence assembly","https://github.com/loneknightpy/idba","Iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data","conda","false","false" +"IGV","2.8.10-conda,2.5.3-shell","sequence-visualisation","Data visualisation","http://software.broadinstitute.org/software/igv/book/export/html/6","Integrative Genomics Viewer (IGV)","conda,shell","false","false" +"igvtools","2.5.3-conda","formatting","Bioinformatics","https://software.broadinstitute.org/software/igv/igvtools","The igvtools utility provides a set of tools for pre-processing data files.","conda","false","false" +"Illumina_utils","2.3-conda","data-handling","Bioinformatics","https://github.com/merenlab/illumina-utils","a small library and a bunch of clients to perform various operations on FASTQ files","conda","false","false" +"Infernal","1.1.3-conda","sequence-analysis","Sequence analysis","http://eddylab.org/infernal/","Infernal is for searching DNA sequence databases for RNA structure and sequence similarities","conda","false","false" +"instaGRAAL","0.1.2-shell","genome-assembly,scaffolding","Sequence assembly","https://github.com/koszullab/instaGRAAL","Large genome reassembly based on Hi-C data","shell","false","false" +"InterProScan","5.48-83.0-singularity,5.28-67.0-shell","sequence-annotation","Functional genomics","http://www.ebi.ac.uk/interpro/about.html","the software package that allows sequences to be scanned against InterPro's signatures","singularity,shell","false","false" +"iq-tree","2.0.3-conda,1.6.7-conda,1.5.5.1-conda","phylogenetic-tree-construction","Phylogeny","http://www.iqtree.org/","Stochastic algorithm to infer phylogenetic trees by maximum likelihood.","conda","true","false" +"isoseq3","3.4.0-conda","splice_transcript_prediction","Transcriptomics","https://github.com/PacificBiosciences/IsoSeq","Scalable De Novo Isoform Discovery","conda","false","false" +"ivar","1.2.2-conda","variant-classification","Biological databases","https://github.com/CGR-UNIMORE/iVar","Interpretation-oriented tool to manage the update and revision of variant annotation and classification.","conda","true","false" +"JBrowse","1.12.3-conda","genome-visualisation","Data visualisation","https://jbrowse.org/","Genome browser","conda","false","false" +"JBrowse2","1.0.2-singularity","genome-visualisation","Data visualisation","https://jbrowse.org/jb2/","Genome browser","singularity","false","false" +"jcvi","0.9.14-conda","genome-assembly,scaffolding","Sequence assembly","https://github.com/tanghaibao/jcvi","Python utility libraries on genome assembly, annotation and comparative genomics ","conda","false","false" +"jellyfish","2.2.6-conda,2.2.10-conda","k-mer-counting","Sequence assembly","http://www.genome.umd.edu/jellyfish.html","A command-line algorithm for counting k-mers in DNA sequence.","conda","false","false" +"Jinja2","2.11.1-conda","data-handling","Data visualisation","https://jinja.palletsprojects.com/en/master/","Jinja is a fast, expressive, extensible templating engine.","conda","false","false" +"jModelTest2","2.1.10-shell","phylogenetic-tree-construction","Phylogeny","https://github.com/ddarriba/jmodeltest2","Tool to carry out statistical selection of best-fit models of nucleotide substitution","shell","false","false" +"Kaiju","1.8.2-conda,1.7.3-conda,1.7.1-conda","taxonomic-classification","Metagenomics","https://github.com/bioinformatics-centre/kaiju/blob/master/README.md","Fast and sensitive taxonomic classification for metagenomics","conda","false","false" +"Kalign","2.04-shell","multiple-sequence-alignment","Phylogeny","http://msa.cgb.ki.se/cgi-bin/msa.cgi","A fast and accurate multiple sequence alignment algorithm","shell","false","false" +"kallisto","0.46.2-conda","gene-expression-profiling","Transcriptomics","https://pachterlab.github.io/kallisto/about.html","A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.","conda","false","false" +"kat","2.4.2-conda","sequence-composition-calculation","Sequence assembly","http://www.earlham.ac.uk/kat-tools","Suite of tools that generate, analyse and compare k-mer spectra produced from sequence files","conda","false","false" +"KEGGDecoder","master-conda","data-handling","Bioinformatics","https://github.com/bjtully/BioData/tree/master/KEGGDecoder","Designed to parse through a KEGG-Koala outputs (blastKOALA, ghostKOALA, KOFAMSCAN) to determine the completeness of various metabolic pathways.","conda","false","false" +"KING","2.8.1-shell","genotyping","Genotype and phenotype","http://people.virginia.edu/~wc9c/KING/","Relationship inference in genome-wide association studies","shell","false","false" +"KisSplice","2.4.0-p1-conda","transcriptome-assembly","Transcriptomics","http://kissplice.prabi.fr/","A local transcriptome assembler for SNPs, indels and AS events","conda","false","false" +"KMC","3.1.2rc1-conda","k-mer-counting","Sequence assembly","https://github.com/refresh-bio/KMC","Fast and frugal disk based k-mer counter ","conda","false","false" +"KmerGenie","1.7016-conda","k-mer-counting","Sequence assembly","http://kmergenie.bx.psu.edu/","estimates the best k-mer length for genome de novo assembly.","conda","false","false" +"KofamScan","1.3.0-conda","expression-profile-pathway-mapping,protein-feature-detection","Gene and protein families","https://github.com/takaram/kofam_scan","KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model.","conda","false","false" +"Kraken2","2.1.1-conda,2.0.9beta-conda","taxonomic-classification","Metagenomics","https://ccb.jhu.edu/software/kraken2/","a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds","conda","false","false" +"KrakenUniq","0.5.8-conda","taxonomic-classification","Metagenomics","https://github.com/fbreitwieser/krakenuniq/blob/master/README.md","Confident and fast metagenomics classification using unique k-mer counts","conda","false","false" +"Krona","2.8.1-conda,2.7-conda","visualisation","Data visualisation","https://sourceforge.net/p/krona/home/krona/","Hierarchical data browser","conda","true","false" +"lbzip2","2.5-conda","data-handling","Bioinformatics","http://lbzip2.org/","lbzip2 is a free, multi-threaded compression utility with support for bzip2 compressed file format","conda","false","false" +"LEfSe","1.0.8-conda","community-profiling","Metagenomics","https://bitbucket.org/biobakery/biobakery/wiki/lefse","Find biomarkers between 2 or more groups using relative abundances","conda","true","false" +"Lep-MAP3","0.2-shell","linkage-analysis","Population genetics","https://sourceforge.net/p/lep-map3/wiki/Home/","a linkage map construction software suite","shell","false","false" +"LINKS","1.8.6-shell","scaffolding","Sequence assembly","http://www.bcgsc.ca/platform/bioinfo/software/links","Long Interval Nucleotide K-mer Scaffolder","shell","false","false" +"lofreq","2.1.5-conda","variant-calling","Comparative genomics","http://csb5.github.io/lofreq/","A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data","conda","false","false" +"longshot","0.4.3-singularity,0.4.2-singularity,0.4.1-conda","variant-calling","Comparative genomics","https://github.com/pjedge/longshot","Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT).","singularity,conda","false","false" +"LRA","1.3.2-conda","sequence-alignment","Sequence assembly","https://github.com/ChaissonLab/LRA","Long read aligner for sequences and contigs","conda","false","false" +"lulu","0.1-conda","sequence-clustering","Metagenomics","https://github.com/tobiasgf/lulu","A r-package for distribution based post clustering curation of amplicon data","conda","false","false" +"MACS","2.1.1.20160309-conda","chip-seq","Epigenetics","https://github.com/taoliu/MACS/","study genome-wide protein-DNA interactions","conda","true","false" +"MACSE","2.01-conda","multiple-sequence-alignment","Phylogeny","https://bioweb.supagro.inra.fr/macse/","Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons","conda","false","false" +"MAFFT","7.490-conda,7.310-conda,7.245-conda","multiple-sequence-alignment","Phylogeny","https://mafft.cbrc.jp/alignment/software/","Multiple alignment program for amino acid or nucleotide sequences","conda","true","false" +"mamba","0.21.2-conda,0.19.0-conda","data-handling","Bioinformatics","https://github.com/mamba-org/mamba","The Fast Cross-Platform Package Manager.","conda","false","false" +"marginPhase","1.0.0-singularity","haplotype-reconstruction","Sequence assembly","https://github.com/benedictpaten/marginPhase","MarginPhase is a program for simultaneous haplotyping and genotyping","singularity","false","false" +"MarginPolish","1.3.0-conda","sequence-assembly","Sequence assembly","https://github.com/UCSC-nanopore-cgl/MarginPolish","A graph-based assembly polisher","conda","false","false" +"mash","2.3-shell","sequence-distance-matrix-generation","Statistics and probability,Metagenomics","https://github.com/marbl/mash","Fast genome and metagenome distance estimation using MinHash.","shell","true","false" +"Mauve","2.4-conda","genome-alignment","Sequence assembly","http://darlinglab.org/mauve/mauve.html","Multiple genome alignment","conda","false","false" +"maxbin2","2.2.7-conda","read-binning","Metagenomics","https://sourceforge.net/projects/maxbin2/","An automatic tool for binning metagenomics sequences.","conda","false","false" +"MCScanX","2019-09-17-conda","synteny","Comparative genomics","http://chibba.pgml.uga.edu/mcscan2/","Multiple Collinearity Scan toolkit","conda","false","false" +"Medaka","1.4.3-conda,1.3.3-conda,1.2.6-conda,0.11.4-conda","sequencing-error-detection","Sequence assembly","https://github.com/nanoporetech/medaka","Sequence correction provided by ONT Research ","conda","false","false" +"MEGAHIT","1.1.1-conda","genome-assembly","Sequence assembly","https://github.com/voutcn/megahit","Assembler for large and complex metagenomics NGS reads","conda","false","false" +"Megalodon","2.3.3-conda","methylation-analysis","Epigenetics","https://github.com/nanoporetech/megalodon","tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads.","conda","false","false" +"Metabat2","2.12.1-conda","read-binning","Metagenomics","https://bitbucket.org/berkeleylab/metabat/src/master/","workflow framework","conda","false","false" +"metabat2","2.15-conda","read-binning","Metagenomics","https://bitbucket.org/berkeleylab/metabat","MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data.","conda","false","false" +"metadecoder","1.0.8-conda","read-binning","Metagenomics","https://github.com/liu-congcong/MetaDecoder","An algorithm for clustering metagenomic sequences","conda","false","false" +"MetaViralSpades","3.14.1-conda","sequence-assembly","Sequence assembly","http://cab.spbu.ru/software/spades/","An assembly toolkit containing various assembly pipelines","conda","false","false" +"MethPipe","3.4.3-shell","methylation-analysis","Epigenetics","http://smithlabresearch.org/software/methpipe/","Analyzing bisulfite sequencing data (WGBS and RRBS)","shell","false","false" +"methylartist","1.0.5-conda","methylation-analysis","Epigenetics","https://github.com/adamewing/methylartist","Pipeline for performing microbiome analysis from raw DNA sequencing data","conda","false","false" +"MethylDackel","0.6.1-conda","methylation-calling","Epigenetics","https://github.com/dpryan79/MethylDackel","MethylDackel will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them","conda","false","false" +"MethylExtract","1.9.1-docker","methylation-analysis","Epigenetics","http://bioinfo2.ugr.es/MethylExtract/","Methylation maps and SNV calling from whole genome bisulfite sequencing data","docker","false","false" +"metilene","0.2.8-conda","DMR-identification","Epigenetics","https://www.bioinf.uni-leipzig.de/Software/metilene/","Fast and sensitive detection of differential DNA methylation.","conda","false","false" +"MIGRATE-N","0.11.5-shell","population-genomics","Population genetics","http://popgen.sc.fsu.edu/Migrate/Migrate-n.html","Estimation of population sizes and gene flow using the coalescent","shell","false","false" +"miniasm","0.2_r168-conda","genome-assembly","Sequence assembly","https://github.com/lh3/miniasm","Ultrafast de novo assembly for long noisy reads (though having no consensus step) ","conda","false","false" +"minimap2","2.9-conda,2.24-conda,2.23-conda,2.22-conda,2.19-conda,2.18-conda,2.17-conda,2.16-conda","read-mapping","Mapping","https://lh3.github.io/minimap2","A versatile pairwise aligner for genomic and spliced nucleotide sequences","conda","false","false" +"MinIONQC","1.4.2-conda","quality-control","Bioinformatics","https://github.com/roblanf/minion_qc","Fast and effective quality control for MinION and PromethION sequencing data ","conda","false","false" +"MIRA","4.9.6-conda","genome-assembly","Sequence assembly","https://sourceforge.net/p/mira-assembler/wiki/Home/","whole genome shotgun and EST sequence assembler for Sanger, 454, Illumina, IonTorrent data and PacBio","conda","false","false" +"mitobim","1.9.1-conda","genome-assembly","Sequence assembly","https://github.com/chrishah/MITObim","MITObim - mitochondrial baiting and iterative mapping","conda","false","false" +"MLST-Check","2.1.1-docker","multilocus-sequence-typing","Comparative genomics","https://github.com/sanger-pathogens/mlst_check","Multilocus sequence typing by blast using the schemes from PubMLST","docker","false","false" +"mlst","2.19.0-conda","taxonomic-classification","Transcriptomics","http://cge.cbs.dtu.dk/services/MLST/","Multi Locus Sequence Typing from an assembled genome or from a set of reads.","conda","false","false" +"MMseqs2 (mpi)","12-113e3-shell,11.e1a1c-shell","taxonomic-classification,sequence-similarity-search,sequence-clustering","Gene and protein families","https://mmseqs.com","MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. ","shell","false","false" +"MMseqs2","9-d36de-conda,11.e1a1c-conda","taxonomic-classification,sequence-similarity-search,sequence-clustering","Gene and protein families","https://mmseqs.com","MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. ","conda","false","false" +"modbam2bed","0.4.6-conda","methylation-calling","Epigenetics","https://github.com/epi2me-labs/modbam2bed","A program to aggregate modified base counts stored in a modified-base BAM file to a bedMethyl file.","conda","false","false" +"ModelTest-NG","0.1.6-conda","read-binning","Phylogeny","https://github.com/ddarriba/modeltest","A new and scalable tool for the selection of DNA and protein evolutionary models. ","conda","false","false" +"moments","1.0.7-conda","statistics-and-probability","Population genetics","https://bitbucket.org/simongravel/moments","Moment-based solution of the diffusion equation in genetics.","conda","false","false" +"momi","2.1.18-conda","population-structure","Population genetics","https://momi2.readthedocs.io/en/latest/index.html","Python package that computes the expected sample frequency spectrum (SFS), a statistic commonly used in population genetics, and uses it to fit demographic history.","conda","false","false" +"MOSAIK","2.2.26-conda","read-mapping","Mapping","https://github.com/wanpinglee/MOSAIK","Mapping second and third-generation sequencing reads to a reference genome","conda","true","false" +"mosdepth","0.2.7-conda","read-depth-analysis","Sequence assembly","https://github.com/brentp/mosdepth","Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing ","conda","false","false" +"mothur","1.42.1-conda,1.39.5-conda,1.38.1.1-conda","community-profiling","Metagenomics","https://www.mothur.org/","Analyzing 16S rRNA gene sequences","conda","false","false" +"MrBayes","3.2.7-conda","phylogenetic-tree-construction","Phylogeny","http://mrbayes.sourceforge.net/","Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models","conda","true","false" +"MrBayes","3.2.6-conda","phylogenetic-tree-construction","Phylogeny","http://mrbayes.sourceforge.net/","Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models","conda","true","false" +"MultiNanopolish","master-conda","sequence-analysis,genetic-variation-analysis","Sequence assembly","https://github.com/BioinformaticsCSU/MultiNanopolish","Software package for signal-level analysis of Oxford Nanopore sequencing data using a different iterative calculation strategy than the original Nanopolish tool to reduce redundant calculation.","conda","false","false" +"multiqc","1.9-conda,1.8-conda,1.5-conda,1.2-conda,1.12-conda,1.11-conda","validation","Bioinformatics","http://multiqc.info/","MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report.","conda","false","false" +"MUMmer","4.0.0beta2-conda,3.23-conda","genome-alignment","Sequence assembly","https://github.com/mummer4/mummer","Versatil alignment tool for DNA and protein sequences","conda","false","false" +"muscle","3.8-conda","multiple-sequence-alignment","Phylogeny","https://www.ebi.ac.uk/Tools/msa/muscle/","MUltiple Sequence Comparison by Log- Expectation","conda","false","false" +"nano","2.2.6-shell","editing","Bioinformatics","https://www.nano-editor.org/dist/v3/nano.html","Simple text editor","shell","false","false" +"NanoCaller","0.4.0-conda,0.3.3-conda","snp-detection","Comparative genomics","https://github.com/WGLab/NanoCaller","A computational method that integrates long reads in deep convolutional neural network for the detection of SNPs/indels from long-read sequencing data","conda","false","false" +"NanoFilt","2.7.1-conda,2.6.0-conda","data-handling","Bioinformatics","https://github.com/wdecoster/nanofilt","Streaming script for filtering a fastq file based on a minimum length, minimum quality cut-off, minimum and maximum average GC","conda","false","false" +"NanoPlot","1.32.1-conda,1.28.0-conda","quality-control","Bioinformatics","https://github.com/wdecoster/NanoPlot","Creating many relevant plots derived from reads (fastq), alignments (bam) and albacore/guppy summary files","conda","false","false" +"Nanopolish","0.13.2-conda","sequence-analysis,genetic-variation-analysis","Sequence assembly","https://github.com/jts/nanopolish","Software package for signal-level analysis of Oxford Nanopore sequencing data.","conda","false","false" +"ncbi-datasets-pylib","10.2.0-conda","data-handling","Bioinformatics","https://pypi.org/project/ncbi-datasets-pylib/","Easily gather data from across NCBI databases","conda","false","false" +"NextDenovo","2.4.0-singularity","genome-assembly","Sequence assembly","https://github.com/Nextomics/NextDenovo","A string graph-based de novo assembler for long reads (CLR, HiFi and ONT).","singularity","false","false" +"Nextflow","21.04.0-conda,20.10.0-conda,20.07.1-conda,20.04.1-conda,20.01.0-conda,19.07.0-conda,18.10.1-conda","workflows","Bioinformatics","https://www.nextflow.io/docs/latest/basic.html","workflow framework","conda","false","false" +"NF-CORE","1.9-conda","workflows","Bioinformatics","https://nf-co.re/tools","Nextflow community tools","conda","false","false" +"NGSUtils","0.5.9-conda","data-handling","Bioinformatics","http://ngsutils.org/","Suite of software tools for working with next-generation sequencing datasets","conda","false","false" +"npScarf","2019.09-conda","scaffolding","Sequence assembly","https://github.com/mdcao/npScarf","Scaffolding and Completing Assemblies in Real-time Fashion","conda","false","false" +"ntEdit","1.3.5-conda","genome-assembly","Sequence assembly","https://github.com/bcgsc/ntedit","Scalable genomics application for polishing genome assembly drafts. It simplifies polishing and haploidization of gene and genome sequences with its re-usable Bloom filter design.","conda","false","false" +"OAU","1.2-shell","sequence-similarity","Comparative genomics","https://www.ezbiocloud.net/tools/orthoaniu","Average nucleotide identity (ANI) calculator, which uses the improved ANI algorithm (OrthoANI) with USEARCH","shell","false","false" +"Obitools","1.0-singularity","community-profiling","Metagenomics","https://git.metabarcoding.org/obitools/obitools/wikis/home","A set of tools to analyse Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding","singularity","false","false" +"Octopus","0.6.3b-conda","variant-calling,haplotype-mapping","Comparative genomics","https://github.com/luntergroup/octopus","Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework","conda","false","false" +"Oligotyping","2.1-conda","community-profiling","Metagenomics","http://merenlab.org/software/oligotyping/","Investigate diversity within their OTUs at a precise level by utilizing subtle variations among 16S Ribosomal RNA gene sequences","conda","false","false" +"ont_fast5_api","3.3.0-conda","data-handling","Bioinformatics","https://github.com/nanoporetech/ont_fast5_api","a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format","conda","false","false" +"OPERA-LG","2.0.6-conda","scaffolding","Sequence assembly","https://sourceforge.net/projects/operasf/","A program for scaffolding of large, repeat-rich eukaryotic genomes","conda","false","false" +"ORSON","1.0.0-Nextflow","sequence-annotation","Transcriptomics,Proteomics,Workflows","https://github.com/ifremer-bioinformatics/orson","A Nextflow workflow to annotate proteome and transcriptome.","Nextflow","false","false" +"OrthoFinder","2.4.0-conda","genome-comparison","Comparative genomics","https://github.com/davidemms/OrthoFinder","OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees","conda","false","false" +"p7zip","16.02-conda","data-handling","Bioinformatics","https://anaconda.org/conda-forge/p7zip","file compressor/decompressor relying on 7zip","conda","false","false" +"P_RNA_scaffolder","2019.09-shell","scaffolding","Sequence assembly","https://github.com/CAFS-bioinformatics/P_RNA_scaffolder","Use paired-end transcriptome reads to scaffold genomes","shell","false","false" +"pairtools","0.3.0-conda","data-handling","Sequence assembly,Epigenetics","https://github.com/open2c/pairtools","CLI tools to process mapped Hi-C data","conda","false","false" +"PAL_FINDER","0.02.04-conda","variant-calling","Comparative genomics","https://sourceforge.net/projects/palfinder/","Finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads, and designs PCR primers to amplify these repeat loci in an automated fashion","conda","false","false" +"pb-assembly/Falcon","0.0.8-0-conda","genome-assembly","Sequence assembly","https://github.com/PacificBiosciences/pb-assembly","FALCON is a diploid-aware assembler which follows the hierarchical genome assembly process (HGAP) and is optimized for large genome assembly though microbial genomes can also be assembled","conda","false","false" +"pbccs","6.0.0-conda","sequence-alignment","Sequence assembly","https://github.com/PacificBiosciences/ccs","CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)","conda","false","false" +"pbcoretools","0.2.4-conda","data-handling","Bioinformatics","https://github.com/PacificBiosciences/pbbioconda","CLI tools and add-ons for PacBio's core APIs (incl dataset)","conda","false","false" +"pbmm2","1.4.0-conda","pairwise-sequence-alignment","Mapping","https://github.com/PacificBiosciences/pbmm2","pbmm2 is a SMRT C++ wrapper for minimap2's C API. pbmm2 is the official replacement for BLASR.","conda","false","false" +"PCAdapt","3.0.4-conda","gene-prediction","Functional genomics","http://membres-timc.imag.fr/Michael.Blum/PCAdapt.html","Genome scan for detecting genes involved in local adaptation","conda","false","false" +"PCAngsd","0.985-conda","population-structure","Population genetics","https://github.com/Rosemeis/pcangsd","Framework for analyzing low depth next-generation sequencing data in heterogeneous populations using PCA","conda","false","false" +"PEAR","0.9.6-conda","read-preprocessing","Bioinformatics"," https://sco.h-its.org/exelixis/web/software/pear/doc.html","An ultrafast, memory-efficient and highly accurate pair-end read merger","conda","false","false" +"PEPPER-Margin-DeepVariant","r0.5-singularity,r0.4-singularity","Oxford Nanopore and PacBio HiFi variant calling","Comparative genomics","https://github.com/kishwarshafin/pepper","PEPPER-Margin-DeepVariant is a haplotype-aware variant calling pipeline for long reads.","singularity","false","false" +"PfamScan","1.6-conda","sequence-similarity-search","Functional genomics","https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/PfamScan+Help+and+Documentation","Search a sequence against a library of Pfam hidden Markov models (HMM)","conda","false","false" +"PHYLIP","3.696-conda","phylogenetic-tree-construction","Phylogeny","http://evolution.genetics.washington.edu/phylip.html","Inferring parsimony phylogenies","conda","true","false" +"phyloFlash","3.4-conda","sequence-assembly","Metagenomics","https://github.com/HRGV/phyloFlash","A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an Illumina (meta)genomic or transcriptomic dataset.","conda","false","false" +"phyloscanner","1.8.0-conda","data-handling","Mapping,Population genetics","https://github.com/BDI-pathogens/phyloscanner","Analysing pathogen genetic diversity and relationships between and within hosts.","conda","false","false" +"PhyML","3.3.2-conda,3.1-shell","phylogenetic-tree-construction","Phylogeny","http://www.atgc-montpellier.fr/phyml/","Estimate Maximum-Likelihook Phylogenies","conda,shell","false","false" +"Picard","2.21.1-conda","data-handling","Bioinformatics","https://github.com/broadinstitute/picard","A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats","conda","false","false" +"PICRUSt","1.1.0-conda","functional-predictions","Metagenomics","http://picrust.github.io/picrust/","Predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.","conda","false","false" +"PICRUSt2","2.4.1-conda","functional-predictions","Metagenomics","https://github.com/picrust/picrust2","Predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.","conda","false","false" +"pigz","2.4-conda","data-handling","Bioinformatics","https://zlib.net/pigz/","A parallel implementation of gzip for modern multi-processor, multi-core machines","conda","false","false" +"Pilon","1.24-conda,1.23-conda","sequencing-error-detection","Sequence assembly","https://github.com/broadinstitute/pilon/","Pilon is an automated genome assembly improvement and variant detection tool ","conda","false","false" +"Planemo","0.70.0-conda","data-handling","Bioinformatics","https://planemo.readthedocs.io/en/latest/","Command-line utilities to assist in building tools for the Galaxy project","conda","false","false" +"PLASS","2.7.35-conda","sequence-assembly","Sequence assembly","https://github.com/soedinglab/plass","Protein-Level ASSembler ","conda","false","false" +"PLAST","2.3.3-shell,2.3.2-shell","sequence-similarity-search","Biological databases","https://plast.inria.fr/user-guide/","High Performance Parallel Local Alignment Search Tool","shell","true","false" +"Platanus","2.0.2-conda,1.2.4-shell","genome-assembly","Sequence assembly","http://platanus.bio.titech.ac.jp/","Genome assembler","conda,shell","false","false" +"Platon","1.3.1-conda,1.2.1-conda","genome-assembly","Sequence assembly","https://github.com/oschwengers/platon","Identification and characterization of bacterial plasmid contigs from short-read draft assemblies","conda","false","false" +"Platypus variant","0.8.1.2-conda","variant-calling","Comparative genomics","https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data","A Haplotype-Based Variant Caller For Next Generation Sequence Data","conda","false","false" +"PLINK","1.9-shell,1.07-shell","genetic-variation-analysis","GWAS study","http://zzz.bwh.harvard.edu/plink/","whole genome association analysis toolset","shell","true","false" +"PointFinder","2018-05-23-conda","variant-calling","Comparative genomics","https://bitbucket.org/genomicepidemiology/pointfinder","detects chromosomal mutations predictive of drug resistance based on WGS data","conda","false","false" +"PoPoolation2","1201-docker","variant-classification","Comparative genomics","https://sourceforge.net/p/popoolation2/wiki/Main/","Compare allele frequencies for SNPs between two or more populations and to identify significant differences","docker","false","false" +"Porechop","0.2.4-conda","sequence-trimming,demultiplexing","Bioinformatics","https://github.com/rrwick/Porechop","Porechop is a tool for finding and removing adapters from Oxford Nanopore reads.","conda","false","false" +"preseq","2.0.3-conda","prediction-and-recognition","Bioinformatics","http://smithlabresearch.org/software/preseq/","This package is aimed at predicting and number of distinct reads and how many will be expected from additional sequencing using an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.","conda","false","false" +"Prinseq","0.20.4-conda","sequence-trimming","Bioinformatics","http://prinseq.sourceforge.net/manual.html","filter, reformat and trim NGS data","conda","false","false" +"ProbCons","1.12-shell","multiple-sequence-alignment","Phylogeny","http://probcons.stanford.edu/download.html","Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences","shell","false","false" +"Prodigal","2.6.3-conda","gene-prediction","Functional genomics","https://github.com/hyattpd/Prodigal","Fast, reliable protein-coding gene prediction for prokaryotic genomes.","conda","false","false" +"Prokka","1.14.6-conda,1.14.5-conda,1.13.7-conda,1.13-conda,1.12-conda","gene-prediction","Functional genomics","http://www.vicbioinformatics.com/software.prokka.shtml","Annotation of prokaryotic genomes","conda","true","false" +"pronto","2.3.1-conda","ontology_visualisation","Bioinformatics","https://github.com/althonos/pronto","Pronto is a Python library to parse, browse, create, and export ontologies, supporting several ontology languages and formats","conda","false","false" +"PSASS","3.1.0-conda","sequence-assembly-validation","Sequence assembly","https://github.com/SexGenomicsToolkit/PSASS","Software to compare pooled sequencing datasets from two groups (usually two sexes).","conda","false","false" +"pycoQC","2.5.2-conda,2.5.0.19-conda","quality-control","Bioinformatics","https://github.com/a-slide/pycoQC","pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)","conda","true","false" +"pyScaf","0.12a-conda","scaffolding","Sequence assembly","https://github.com/lpryszcz/pyScaf","Orders contigs from genome assemblies","conda","false","false" +"qcat","1.1.0-conda","demultiplexing","Bioinformatics","https://github.com/nanoporetech/qcat","qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files. ","conda","false","false" +"QIIME","2021.11-conda,2021.08-conda,2020.08-conda,2020.02-conda,2019.10-conda,2019.07-conda,2019.04-conda,2.0.0-conda,1.9.1-conda","community-profiling","Metagenomics","http://qiime.org/","Pipeline for performing microbiome analysis from raw DNA sequencing data","conda","false","false" +"qualimap","2.2.2d-conda","sequencing-quality-control","Data visualisation","http://qualimap.bioinfo.cipf.es/","Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.","conda","true","false" +"QuasiRecomb","1.2-conda","recombination-detection","DNA replication and recombination","https://github.com/cbg-ethz/QuasiRecomb","Probabilistic inference of viral quasispecies subject to recombination (viral haplotype reconstruction)","conda","false","false" +"QUAST","5.0.2-conda,5.0.0-conda,4.6.3-conda,4.5-conda","sequence-assembly-validation","Sequence assembly","http://bioinf.spbau.ru/quast","Evaluates genome assemblies","conda","false","false" +"r-metabarcoding-toolbox","1.0-conda","community-profiling","Metagenomics","https://w3z.ifremer.fr/bioinfo/Cmdline-Datarmor/Ressources-disponibles/Les-toolboxes-creees-a-facon/R-Metabarcoding-toolbox","Homemade toolbox with common tools used in R for metabacording analysis","conda","false","false" +"r","4.1.1-conda,4.0.0-conda,3.6.1-conda,3.5.1-conda","statistics-and-probability,visualisation","Statistics and probability","https://www.r-project.org/","R base","conda","false","false" +"ra","0.2.1-shell","genome-assembly","Sequence assembly","https://github.com/lbcb-sci/ra","Overlap-layout-consensus based DNA assembler of long uncorrected reads (short for Rapid Assembler).","shell","false","false" +"Racon","1.4.20-conda,1.4.10-conda","sequencing-error-detection","Sequence assembly","https://github.com/lbcb-sci/racon","Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads ","conda","false","false" +"ragout","2.3-conda","genome-assembly","Sequence assembly","http://fenderglass.github.io/Ragout/","Tool for assisted assembly using multiple references. It takes a short read assembly (a set of contigs), a set of related references and a corresponding phylogenetic tree and then assembles the contigs into scaffolds.","conda","false","false" +"RagTag","1.0.2-conda","genome-assembly","Sequence assembly","https://github.com/malonge/RagTag","Reference-guided genome assembly correction and scaffolding","conda","false","false" +"Raven","1.5-conda,0.0.7-conda","genome-assembly","Sequence assembly","https://github.com/lbcb-sci/raven","De novo genome assembler for long uncorrected reads","conda","false","false" +"RAxML","8.2.12-conda","phylogenetic-tree-construction","Phylogeny","https://sco.h-its.org/exelixis/web/software/raxml/index.html","Randomized Axelerated Maximum Likelihood.","conda","false","false" +"Rcorrector","1.0.4-conda,1.0.3-conda","read-correction","Sequence assembly","https://github.com/mourisl/Rcorrector","kmer-based error correction method for RNA-seq data","conda","true","false" +"rdp_classifier ","2.2-conda","taxonomic-classification","Metagenomics","http://rdp.cme.msu.edu/","Naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain to genus","conda","false","false" +"rdp_classifier","2.13-conda","taxonomic-classification","Metagenomics","http://rdp.cme.msu.edu/","Naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain to genus","conda","false","false" +"remoVecSec","0.02-conda","sequence-contamination-filtering","Biological databases","https://github.com/htafer/remoVecSec","Module and script to remove contamination in assembled genomes before submission to ncbi ","conda","false","false" +"RpARK","1.3.0-conda","repeat-sequence-analysis","Sequence composition, complexity and repeats","https://github.com/PhKoch/RepARK","wrapper script for constructing a repeat library from sequencing reads","conda","false","false" +"REPdenovo","0.0.1-conda","repeat-sequence-analysis","Sequence composition, complexity and repeats","https://github.com/simoncchu/REPdenovo","constructing repeats directly from sequence reads","conda","false","false" +"RepeatModeler","2.0.1-conda,1.0.11-conda","repeat-sequence-analysis","Sequence composition, complexity and repeats","https://github.com/rmhubley/RepeatModeler","De-Novo Repeat Discovery Tool","conda","false","false" +"RGI","5.1.1-conda","gene-prediction","Functional genomics","https://github.com/arpcard/rgi","Resistance Gene Identifier (RGI) predicts resistome(s) from protein or nucleotide data based on homology and SNP models","conda","true","false" +"roary","3.13.0-conda","genome-assembly","Mapping","http://sanger-pathogens.github.io/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.","conda","true","false" +"RStudio","1.1.456-conda","statistics-and-probability,visualisation","Statistics and probability","https://rstudio.com/","Tool for statistics","conda","false","false" +"salmon","1.6-conda,1.5.2-conda,1.3.0-conda,0.14.1-conda,0.13.1-conda","rna-seq-quantification","Transcriptomics","https://combine-lab.github.io/salmon/","quantifying the expression of transcripts using RNA-seq data","conda","true","false" +"SALSA2","2.3-conda","genome-assembly,scaffolding","Sequence assembly","https://github.com/marbl/SALSA","A tool to scaffold long read assemblies with Hi-C data","conda","false","false" +"SAMBA-ROME","1.0.0-Nextflow","community-profiling","Metagenomics,Workflows","https://github.com/ifremer-bioinformatics/samba-rome","Workflow for the standardized and automated analyses of the metabarcoding data from the ROME project.","Nextflow","false","false" +"SAMBA","3.0.1-Nextflow,2.0.0-Nextflow","community-profiling","Metagenomics,Workflows","https://github.com/ifremer-bioinformatics/samba","Standardized and Automated MetaBarcoding Analyses.","Nextflow","false","false" +"sambamba","0.8.0-conda,0.6.6-conda","data-handling","Bioinformatics","https://github.com/biod/sambamba","parallel robust and fast tool for working with SAM and BAM files","conda","false","false" +"samblaster","0.1.26-conda","split-read-mapping","Mapping","https://github.com/GregoryFaust/samblaster","A tool to mark duplicates and extract discordant and split reads from SAM files.","conda","false","false" +"SAMtools","1.9-conda,1.6-conda,1.4.1-conda,1.14-conda,1.13-conda,1.11-conda,1.10-conda","data-handling","Bioinformatics","http://samtools.sourceforge.net/","Provides various utilities for manipulating alignments in the SAM format","conda","false","false" +"sartools","1.7.3-conda,1.6.3-conda,1.3.2-conda","statistical-calculation","Transcriptomics","https://github.com/PF2-pasteur-fr/SARTools","A tool for statistical analysis of RNA-Seq","conda","true","false" +"Scrappie","1.4.2-conda","base-calling","Sequence assembly","https://github.com/nanoporetech/scrappie","Technology demonstrator for the Oxford Nanopore Research Algorithms group","conda","false","false" +"seqc","0.2.5-conda","rna-seq-analysis,quality-control","Transcriptomics","https://github.com/dpeerlab/seqc","Single-Cell Sequencing Quality Control and Processing Software","conda","false","false" +"seqkit","2.1.0-conda,2.0.0-conda,0.9.1-conda","data-handling","Bioinformatics","https://bioinf.shenwei.me/seqkit","Tool to manipulate fastq files","conda","false","false" +"SeqTk","1.3-conda,1.2-conda","data-handling","Bioinformatics","https://github.com/lh3/seqtk","A fast and lightweight tool for processing sequences in the FASTA or FASTQ format","conda","true","false" +"SGA","0.10.15-conda","genome-assembly","Sequence assembly","https://github.com/jts/sga","De novo sequence assembler using string graphs","conda","false","false" +"SHAPEIT4","4.2.0-conda","haplotype-mapping","Genotype and phenotype","https://odelaneau.github.io/shapeit4/","fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data","conda","false","false" +"shasta","0.4.0-shell","genome-assembly","Sequence assembly","https://github.com/chanzuckerberg/shasta","De novo assembly from Oxford Nanopore reads.","shell","false","false" +"ShoRAH","1.1.0-conda","variant-calling,haplotype-mapping","Comparative genomics","https://github.com/cbg-ethz/shorah","Short Reads Assembly into Haplotypes","conda","false","false" +"shovill","1.1.0-conda,1.0.9-conda","genome-assembly","Sequence assembly","https://github.com/tseemann/shovill","Microbial assembly pipeline for Illumina paired-end reads","conda","true","false" +"signalP","6.0g-singularity,5.0b-shell,4.1-shell","sequence-motif-recognition","Structure analysis","http://www.cbs.dtu.dk/services/SignalP/","predicts the presence and location of signal peptide cleavage sites in amino acid sequences ","singularity,shell","false","false" +"Simka","1.4-shell","community-profiling","Metagenomics","https://github.com/GATB/simka","De novo comparative metagenomics tool","shell","false","false" +"slow5tools","0.3.0-conda","data-handling","Bioinformatics","https://github.com/hasindu2008/slow5tools","Slow5tools is a simple toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format, a new file format for storing signal data from Oxford Nanopore Technologies (ONT) devices.","conda","false","false" +"SMRT Tools","5.1.0-shell","workflows","Bioinformatics","http://programs.pacificbiosciences.com/l/1652/2018-03-20/3wrpm7/1652/190674/SMRT_Tools_Reference_Guide__v5.1.0_.pdf","Suite available for analysis of DNA sequencing data from Pacific Biosciences’ SMRT technology","shell","false","false" +"Smudgeplot","0.2.3-conda,0.2.0-conda","quality-control","Sequence assembly","https://github.com/KamilSJaron/smudgeplot","Inference of ploidy and heterozygosity structure using whole genome sequencing data","conda","false","false" +"snakemake","6.6.0-conda,6.4.0-conda,5.4.0-conda,5.10.0-conda","service-composition","Bioinformatics","https://snakemake.readthedocs.io/en/stable/index.html","Workflow engine and language. It aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style.","conda","false","false" +"Sniffles","1.0.7-conda,1.0.12-conda","variant-calling","Comparative genomics","https://github.com/fritzsedlazeck/Sniffles","structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)","conda","false","false" +"Snippy","4.4.0-conda,4.1.0-conda","variant-calling","Comparative genomics","https://github.com/tseemann/snippy","Rapid haploid variant calling and core SNP phylogeny","conda","false","false" +"snpeff","5.0-conda,4.5covid19-conda,4.3.1t-conda,4.3-conda","variant-classification,snp-detection","Comparative genomics","http://snpeff.sourceforge.net/","Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).","conda","true","false" +"snpsift","4.3.1t-conda","variant-filtering","Comparative genomics","http://snpeff.sourceforge.net/SnpSift.html","Toolbox that allows you to filter and manipulate annotated vcf files.","conda","false","false" +"SNVoter","1.0-conda","snp-detection","Comparative genomics","https://github.com/vahidAK/SNVoter","Improving SNV detection from low coverage nanopore sequencing data (<30x)","conda","false","false" +"SOAPdenovo","2.40-conda","genome-assembly","Sequence assembly","http://soap.genomics.org.cn/soapdenovo.html#inst2","short-read assembly method that can build a de novo draft assembly for the human-sized genomes","conda","false","false" +"SortMeRNA","4.2.0-conda,2.1b-conda","read-preprocessing","Bioinformatics","https://github.com/biocore/sortmerna","next-generation sequence filtering and alignment tool","conda","false","false" +"SourceTracker","2.0.1-conda,1.0.1-shell","community-profiling","Metagenomics","https://github.com/danknights/sourcetracker/","Bayesian approach to estimating the proportion of a novel community that comes from a set of source environments","conda,shell","false","false" +"sourmash","2.0.0-conda","sequence-similarity","Bioinformatics","https://github.com/dib-lab/sourmash","Compute MinHash signatures for nucleotide (DNA/RNA) and protein sequences","conda","false","false" +"Spades","3.15.4-conda,3.15.3-conda,3.15.2-conda,3.14.0-conda,3.13.0-conda,3.12.0-conda,3.11.0-conda,3.10.1-conda","sequence-assembly","Sequence assembly","http://cab.spbu.ru/software/spades/","An assembly toolkit containing various assembly pipelines","conda","false","false" +"SRA Toolkit","2.10.1-conda","data-handling","Biological databases","https://github.com/ncbi/sra-tools","The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives","conda","false","false" +"SSpace-long read","1.1-conda","scaffolding","Sequence assembly","https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-211","A program for scaffolding pre-assembled contigs using long reads","conda","false","false" +"SSpace-Standard","3.0-conda","scaffolding","Sequence assembly","https://www.baseclear.com/services/bioinformatics/basetools/sspace-standard/","stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data","conda","false","false" +"stacks","2.59-shell,2.55-conda,2.52-conda,2.0Beta9-conda,2.0Beta8-conda,1.46-conda","population-genomics","Population genetics","http://catchenlab.life.illinois.edu/stacks/","An analysis tool set for population genomics","shell,conda","false","false" +"star","2.7.9a-conda,2.7.8a-conda,2.7.2c-conda,2.7.10a-conda,2.7.0d-conda,2.5.3a-conda","read-mapping","Transcriptomics","https://github.com/alexdobin/STAR#manual","A ultrafast universal RNA-seq aligner","conda","false","false" +"Strainberry","1.1-conda","genome-assembly","Sequence assembly","https://github.com/rvicedomini/strainberry#installation","Strain separation in low-complexity metagenomes using error-prone long-read technologies","conda","false","false" +"StringTie","2.1.4-conda","transcriptome-assembly,RNAseq-analysis","Transcriptomics","https://ccb.jhu.edu/software/stringtie/","Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts","conda","false","false" +"Structure","2.3.4-conda","population-genomics","Population genetics","https://web.stanford.edu/group/pritchardlab/structure.html","a free software package for using multi-locus genotype data to investigate population structure","conda","false","false" +"SVIM","2.0.0-conda,1.4.2-conda","variant-calling","Comparative genomics","https://github.com/eldariont/svim","Structural variant identification using long reads","conda","false","false" +"swarm","3.1.0-conda","community-profiling","Metagenomics","https://github.com/torognes/swarm","A robust and fast clustering method for amplicon-based studies.","conda","false","false" +"T-Coffee","11.0.8-conda","multiple-sequence-alignment","Phylogeny","http://www.tcoffee.org/","A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments","conda","true","false" +"tabix","0.2.6-conda","data-handling","Bioinformatics","http://www.htslib.org/doc/tabix.html","Generic indexer for TAB-delimited genome position files ","conda","false","false" +"TaxMapper","1.0.2-conda","genetic-mapping","Mapping","https://bitbucket.org/dbeisser/taxmapper/src/master/","Analysis tool for a reliable mapping to a provided microeukaryotic reference database","conda","false","false" +"taxonkit","0.8.0-conda","data-handling","Bioinformatics","https://github.com/shenwei356/taxonkit","A Practical and Efficient NCBI Taxonomy Toolkit","conda","false","false" +"TEclass","2.3.1b-singularity","transposon-prediction,sequence-annotation","Sequence analysis","http://www.compgen.uni-muenster.de/tools/teclass/index.hbi","TEclass classifies unknown transpsosable element (TE) consensus sequences into four categories, according to their mechanism of transposition: DNA transposons, LTRs, LINEs, SINEs","singularity","false","false" +"TMHMM","2.0-shell","sequence-motif-recognition","Structure analysis","http://www.cbs.dtu.dk/services/TMHMM/","prediction of transmembrane helices in proteins","shell","false","false" +"Tombo","1.5.1-conda","snp-detection","Comparative genomics","https://github.com/nanoporetech/tombo","Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.","conda","false","false" +"tooldirectory","v3.0.0-conda","visualisation","Bioinformatics","https://github.com/ifremer-bioinformatics/ToolDirectory","Dynamic visualization of softwares managed by a Bioinformatics Core Facility","conda","false","false" +"Tophat2","2.1.1-conda","read-mapping","Transcriptomics","https://ccb.jhu.edu/software/tophat/manual.shtml","A fast splice junction mapper for RNA-Seq reads","conda","true","false" +"Trans-ABySS","2.0.1-conda","transcriptome-assembly","Transcriptomics","https://github.com/bcgsc/transabyss","De novo assembly of RNAseq data using ABySS","conda","false","false" +"TransDecoder","3.0.1-conda","gene-prediction,coding-region-prediction","Functional genomics","https://github.com/TransDecoder/TransDecoder/wiki","identifies candidate coding regions within transcript sequences","conda","true","false" +"transrate","1.0.3-conda","sequence-assembly-validation","Transcriptomics","http://hibberdlab.com/transrate/index.html","de-novo transcriptome assembly quality analysis","conda","false","false" +"TreeMix","1.13-conda","phylogenetic-tree-generation,genetic-variation-analysis","Population genetics","https://bitbucket.org/nygcresearch/treemix/wiki/Home","Method for inferring the patterns of population splits and mixtures in the history of a set of populations","conda","false","false" +"Trimgalore","0.6.7-conda,0.6.4-conda,0.6.3-conda,0.4.1-conda","quality-control,sequence-trimming","Bioinformatics","http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf","A tool to automate quality and adapter trimming as well as quality control","conda","false","false" +"Trimal","1.4.1-conda","sequence-trimming","Bioinformatics","http://trimal.cgenomics.org/","A tool for automated alignment trimming in large-scale phylogenetic analyses","conda","true","false" +"Trimmomatic","0.36-conda","sequence-trimming","Bioinformatics","http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf","A flexible trimmer for Illumina sequence data","conda","true","false" +"Trinity","2.8.5-conda,2.8.4-conda,2.5.1-conda,2.4.0-conda","transcriptome-assembly","Transcriptomics","https://github.com/trinityrnaseq/trinityrnaseq/wiki","De novo assembly of RNA-Seq data","conda","false","false" +"Trinotate","3.1.1-conda","sequence-annotation","Transcriptomics","https://github.com/Trinotate/Trinotate","Annotate transcripts generated by Trinity","conda","true","false" +"trnascan-se","2.0.7-conda","trna-gene-prediction","Functional genomics","http://trna.ucsc.edu/tRNAscan-SE/","A program for improved detection of transfer RNA genes in genomic sequence.","conda","false","false" +"Trycycler","0.5.0-conda","genome-assembly","Sequence assembly","https://github.com/rrwick/Trycycler","Tool for generating consensus long-read assemblies for bacterial genomes.","conda","false","false" +"TSEBRA","1.0.3-conda","gene-prediction","Functional genomics","https://github.com/Gaius-Augustus/TSEBRA","TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.","conda","false","false" +"ucsc-bigbedtobed","v377-conda","data-handling","Bioinformatics","http://hgdownload.cse.ucsc.edu/admin/exe/","Convert from bigBed to ascii bed format.","conda","false","false" +"faToTwoBit","357-conda","data-handling","Bioinformatics","https://bioconda.github.io/recipes/ucsc-fatotwobit/README.html","Convert DNA from fasta to 2bit format","conda","false","false" +"UGENE","1.32.0-shell","sequence-visualisation,workflows","Bioinformatics","http://ugene.net/documentation.html","free open-source cross-platform bioinformatics software","shell","false","false" +"Unicycler","0.5.0-conda,0.4.8-conda","genome-assembly","Sequence assembly","https://github.com/rrwick/Unicycler","Assembly pipeline for bacterial genomes","conda","true","false" +"vadr","1.1-singularity","sequence-annotation","Functional genomics","https://github.com/nawrockie/vadr#vadr-documentation-","Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation","singularity","false","false" +"vamb","3.0.3-gpu-conda,3.0.3-conda","scaffolding","Metagenomics,Sequence assembly","https://github.com/RasmussenLab/vamb","Improved metagenome binning and assembly using deep variational autoencoders.","conda","false","false" +"Variabel","1.0.0-conda","variant-calling","Comparative genomics","https://gitlab.com/treangenlab/variabel","Novel approach and method for intrahost variant detection, which outperforms existing ONT variant callers","conda","false","false" +"VarScan","2.4.3-conda","variant-calling","Comparative genomics","http://dkoboldt.github.io/varscan/","variant detection in massively parallel sequencing data","conda","true","false" +"vcflib","1.0.0_rc1-conda","data-handling","Bioinformatics","https://github.com/vcflib/vcflib","provides methods to manipulate and interpret sequence variation as it can be described by VCF","conda","false","false" +"VCFTools","0.1.16-conda,0.1.14-conda","data-handling","Bioinformatics","https://vcftools.github.io/index.html","Program package designed for working with VCF files","conda","false","false" +"Velvet","1.2.10-conda","genome-assembly","Sequence assembly","https://www.ebi.ac.uk/~zerbino/velvet","Sequence assembler for very short reads","conda","true","false" +"VIGA","0.11.0-singularity","sequence-annotation,functional-prediction","Functional genomics","https://github.com/EGTortuero/viga","De novo Viral Genome Annotator. VIGA is a script written in Python 2.7 that annotates viral genomes automatically (using a de novo algorithm) and predict the function of their proteins using BLAST and HMMER","singularity","true","false" +"vsearch","2.11.1-shell","sequence-clustering","Bioinformatics","https://github.com/torognes/vsearch","vectorized search, the open-source alternative to usearch","shell","false","false" +"vt","2015.11.10-conda","variant-calling","Comparative genomics","https://github.com/atks/vt","tool set for short variant discovery in genetic sequence data","conda","false","false" +"vulcan","1.0.3-conda","pairwise-sequence-alignment","Mapping","https://gitlab.com/treangenlab/vulcan","A long read mapping pipeline that melds minimap2 and NGMLR","conda","false","false" +"w2rap-contigger","2019-07-11-shell","sequence-assembly","Sequence assembly","http://bioinfologics.github.io/the-w2rap-contigger/","An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes","shell","false","false" +"wengan","0.1-shell","genome-assembly","Sequence assembly","https://github.com/adigenova/wengan","An accurate and ultra-fast hybrid genome assembler","shell","false","false" +"WhatsHap","1.0-conda,0.18-conda","genome-assembly","Sequence assembly","https://whatshap.readthedocs.io/en/latest/","WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly","conda","false","false" +"WHdenovo","14012020-conda","genome-assembly","Sequence assembly","https://github.com/shilpagarg/WHdenovo","A cost-effective approach to diploid assembly for single samples and trios","conda","false","false" +"Winnowmap","2.03-shell","pairwise-sequence-alignment","Mapping","https://github.com/marbl/Winnowmap","Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.","shell","false","false" +"wtdbg2/Readbean","2.5-conda","genome-assembly","Sequence assembly","https://github.com/ruanjue/wtdbg2","A fuzzy Bruijn graph approach to long noisy reads assembly","conda","false","false" +"yacrd","0.6.0-conda","quality-control","Sequence assembly","https://github.com/natir/yacrd","Yet Another Chimeric Read Detector","conda","false","false" +"yak","0.1-shell","k-mer-counting","Sequence assembly","https://github.com/lh3/yak","Yet another k-mer analyzer ","shell","false","false"