Ifremer-Softwares.csv

Name,Version,Operation,Topic,Doc,Description,Environment,Galaxy,Workflow
"3SEQ","1.7-build170612-shell","sequence-alignment-analysis","Comparative genomics","https://mol.ax/software/3seq/","3SEQ is a command-line program that reads in a nucleotide sequence file, in phylip or aligned fasta format, and tests all sequence triplets in the file for a mosaic recombination signal indicating that one of the three sequences (the child) is a recombinant of the other two (the parents).","shell","false","false"
"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","antimicrobial-resistance-prediction","Genomics,Microbiology","https://github.com/tseemann/abricate","Mass screening of contigs for antimicrobial resistance or virulence genes.","conda","true","false"
"actc","0.2.0-conda","pairwise-sequence-alignment","Mapping","https://github.com/PacificBiosciences/actc","Align subreads to ccs reads","conda","false","false"
"ADMIXTURE","1.3.0-shell","genetic-variation-analysis","Population genetics","http://software.genetics.ucla.edu/admixture/","Maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates using a fast numerical optimization algorithm.","shell","false","false"
"aegean","0.16.0-conda","sequence-annotation","Genomics","http://brendelgroup.github.io/AEGeAn/","The AEGeAn Toolkit provides a bundle of software tools for evaluating gene structure annotations and genome organization.","conda","true","false"
"AGAT","1.0.0-conda,0.8.0-conda","data-handling","Genomics","https://github.com/NBISweden/AGAT","Another Gff Analysis Toolkit (AGAT)","conda","false","false"
"agptools","0.0.1-conda","genome-assembly","Genomics,Sequence assembly","https://warrenlab.github.io/agptools/","Agptools is a suite of tools for performing edits to an AGP file during this manual curation stage of genome assembly.","conda","false","false"
"AlienTrimmer","0.4.2-conda","nucleic-acid-sequence-analysis","Sequence analysis","https://research.pasteur.fr/en/software/alientrimmer/","Trimming and clipping FASTQ-formatted read files.","conda","false","false"
"Alvis","1.2-singularity","chimera-detection","Genomics,Sequence analysis,Imaging","https://github.com/SR-Martin/alvis","Alvis is a tool for contig and read ALignment VISualisation and chimera detection. It produces LaTeX and SVG alignment diagrams from a number of common alignment formats.","singularity","false","false"
"andi","0.13-singularity","sequence-distance-matrix-generation","Phylogenetics","https://github.com/EvolBioInf/andi","andi estimates the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.","singularity","false","false"
"ANGSD","0.933-conda,0.931-conda,0.923-conda","sequence-analysis","Population genetics,Statistics and probability","http://www.popgen.dk/angsd","Software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.","conda","false","false"
"antiSMASH","6.0.1-conda,5.1.2-conda","sequence-clustering","Gene and protein families,Molecular interactions, pathways and networks","http://antismash.secondarymetabolites.org","Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.","conda","false","false"
"anvi'o","7dev-conda,7.1-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","sequence-similarity-search","Sequence analysis,Phylogeny","http://arb-home.de","The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria","conda","false","false"
"ARCS","1.2.4-conda,1.0.5-conda","genome-assembly","Genomics,Sequence assembly","https://github.com/bcgsc/ARCS/","Scaffolding genome assemblies using 10X Genomics Chromium data or stLFR linked reads","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","Genomics","https://github.com/artic-network/fieldbioinformatics","A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore","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","operation,homology-based-gene-prediction,ab-initio-gene-prediction,gene-prediction","Gene transcripts,Gene and protein families","http://bioinf.uni-greifswald.de/augustus","AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.","conda","false","false"
"Autometa","2.0.3-conda","read-binning","Metagenomics","https://github.com/KwanLab/Autometa","An automated binning pipeline for single metagenomes, in particular host-associated and highly complex ones.","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"
"BA3-SNPS-autotune","2.1.2-singularity","population-genomics","Population genetics","https://github.com/stevemussmann/BA3-SNPS-autotune","This program will automatically tune mixing parameters for BA3-SNPs by implementing a binary search algorithm and conducting short exploratory runs of BA3-SNPS.","singularity","false","false"
"bakta","1.5.1-conda,1.5-conda","genome-annotation","Genomics,Sequence analysis,Data submission, annotation and curation","https://github.com/oschwengers/bakta","Rapid & standardized annotation of bacterial genomes & plasmids","conda","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","formatting","Sequence analysis,Data management,Sequencing","https://gsl.hudsonalpha.org/information/software/bam2fastq","Extract reads from a bam file and write them in fastq format.","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","Data management,Sequence analysis,Sequencing","https://github.com/pezmaster31/bamtools","BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.","conda","false","false"
"bamUtil","1.0.14-conda","data-handling","Data management","http://genome.sph.umich.edu/wiki/BamUtil","Bamutil provides a serie of programs to work on SAM/BAM files.","conda","false","false"
"Bandage","0.8.1-conda","sequence-assembly-visualisation","Genomics,Sequence assembly","https://rrwick.github.io/Bandage/","GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.","conda","true","false"
"barrnap","0.9-conda","gene-prediction","Model organisms,Genomics","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"
"batiscaf","1eddb25-conda","scaffolding","Sequence assembly","https://github.com/mandricigor/batiscaf","BATISCAF is a novel repeat aware scaffolding tool","conda","false","false"
"baypass","2.3-conda","genetic-variation-analysis","Genomics,Genetics,Biomarkers,Population genomics","http://www1.montpellier.inra.fr/CBGP/software/baypass/index.html","This package is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).","conda","false","false"
"cutadapt","38.57-conda,1.18-conda","sequence-trimming","Genomics,Probes and primers,Sequencing","https://pypi.python.org/pypi/cutadapt","Find and remove 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,1.16-conda,1.13-conda,1.10.2-conda","data-handling","DNA polymorphism,Genetic variation,GWAS study,Genotyping experiment","http://www.htslib.org/","BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.","conda","true","false"
"Beagle","4.0_06Jun17-conda","phasing","Population genetics","https://faculty.washington.edu/browning/beagle/beagle.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"
"BEAST","1.10.4-conda","multiple-sequence-alignment","Phylogenetics,Sequence analysis","http://beast.bio.ed.ac.uk/","The Bayesian Evolutionary Analysis Sampling Trees is a cross-platform program for Bayesian analysis of molecular sequences using MCMC (Markov chain Monte Carlo). It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.","conda","false","false"
"beast2","2.6.3-conda","phylogenetic-tree-reconstruction","Phylogenetics,Phylogenomics","http://www.beast2.org","Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. It uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. It includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.","conda","false","false"
"BEDOPS","2.4.38-conda","sequence-annotation","Nucleic acids,Sequence sites, features and motifs","https://bedops.readthedocs.io/en/latest/","BEDOPS is an open-source command-line toolkit that performs efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.","conda","false","false"
"bedtools","2.30.0-conda,2.27.1-conda,2.26.0-conda","mapping","Genomics","https://github.com/arq5x/bedtools2","BEDTools is an extensive suite of utilities for comparing genomic features in BED format.","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"
"Bellerophon","1.0-conda","de-novo-assembly","Workflows,Transcriptomics,Sequence assembly,RNA-Seq","https://github.com/JesseKerkvliet/Bellerophon","The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras.","conda","true","false"
"best","0.1.0-conda","sequence-alignment-validation","Sequence analysis,Bioinformatics","https://github.com/google/best","Bam Error Stats Tool (best): analysis of error types in aligned reads.","conda","false","false"
"BiG-SCAPE / CORASON","1.1.4-conda","sequence-clustering","Phylogeny","https://bigscape-corason.secondarymetabolites.org/tutorial/index.html","BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.","conda","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","1.34.0-conda,1.20.0-conda,1.14.1-conda","differential-gene-expression-analysis","Transcriptomics","http://bioconductor.org/packages/DESeq2/","R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.","conda","true","false"
"methylKit","0.99.2-conda","methylation-analysis","Epigenetics,DNA,Methylated DNA immunoprecipitation","http://bioconductor.org/packages/release/bioc/html/methylKit.html","R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Perl is needed to read SAM files only.","conda","true","false"
"phyloseq","1.14.2-conda","deposition","Sequence analysis,Microbiology,Metagenomics","http://bioconductor.org/packages/release/bioc/html/phyloseq.html","Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.","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"
"bioconvert","0.6.3-conda","Bioinformatics","data-handling","https://github.com/bioconvert/bioconvert","Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.","conda","false","false"
"biom-format","2.1.6-conda","conversion","Bioinformatics","http://biom-format.org/documentation/biom_conversion.html","Converting between file formats","conda","true","false"
"Bionano Solve","1.7.0-singularity","genome-assembly,de-novo-assembly,scaffolding","Sequence assembly,DNA binding sites,Mapping","https://bionanogenomics.com","Bionano Solve is a set of tools for analyzing Bionano data (generated from Saphyr and Irys).","singularity","true","false"
"Bioperl","1.7.2-conda","data-handling","Genomics,Data management,Software engineering","http://bioperl.org/","A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.","conda","false","false"
"Biopython","1.79-conda,1.78-conda,1.70-conda","deposition","Bioinformatics,Data management,Computational biology,Software engineering","http://biopython.org/","Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.","conda","false","false"
"Bismark","0.23.1-conda,0.20.0-conda,0.19-conda,0.17-conda","methylation-analysis","Genomics,Epigenetics,Epigenomics","https://github.com/FelixKrueger/Bismark","Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.","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","local-alignment,mapping","Genomics,Mapping,Sequencing","https://github.com/PacificBiosciences/blasr","Software for mapping Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error.","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","deposition","Sequence assembly,Workflows,Zoology,Model organisms,Phylogenomics","https://blobtoolkit.genomehubs.org/view","BlobToolKit Viewer is a genome-scale dataset visualistion tool developed as part of the blobtoolkit project to allow browser-based identification and filtering of target and non-target data in genome assemblies.","singularity","false","false"
"blobtools","2.6.3-conda,1.1-conda","sequence-assembly-visualisation","Genomics,Data management,Sequence assembly","https://github.com/DRL/blobtools","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","Genomics,Mapping","http://bowtie-bio.sourceforge.net/bowtie2/index.shtml","Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.","conda","true","false"
"bracken","2.8-conda","statistical-calculation","Microbial ecology,Metagenomics","https://ccb.jhu.edu/software/bracken/","Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.","conda","false","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"
"braker3","3.0.2-singularity","genome-annotation","RNA-Seq,Workflows,RNA","http://bioinf.uni-greifswald.de/bioinf/braker/index.html","Pipeline for unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS.","singularity","false","false"
"BS-SNPer","master-docker","snp-detection","DNA polymorphism,DNA,Statistics and probability","https://github.com/hellbelly/BS-Snper","An ultrafast and memory-efficient package, a program for BS-Seq variation detection from alignments in standard BAM/SAM format using approximate Bayesian modeling.","docker","false","false"
"bsmap","2.90-conda","read-mapping","Epigenetics","https://code.google.com/archive/p/bsmap/","short reads mapping software for bisulfite sequencing","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","5.4.3-conda,5.4.0-conda,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","Genomics,Transcriptomics,Sequence assembly,Sequence analysis","http://busco.ezlab.org/","Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.","conda","false","false"
"bwa-mem2","2.2.1-conda,2.1-conda","sequence-alignment","Mapping","https://github.com/bwa-mem2/bwa-mem2","Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.","conda","false","false"
"BWA","0.7.17-conda,0.7.15-conda","generation,sequence-alignment,genome-indexing,read-mapping","Mapping","http://bio-bwa.sourceforge.net","Fast, accurate, memory-efficient aligner for short and long sequencing reads","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","de-novo-assembly","Genomics","https://github.com/marbl/canu","De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.","conda","false","false"
"cap3","10.2011-conda","genome-assembly","Genetic variation,Sequence analysis,Sequence assembly,Sequencing","http://biosrv.cab.unina.it/webcap3/","Web-based contig assembly.","conda","false","false"
"cd-hit","4.8.1-shell","sequence-clustering","Sequencing","https://github.com/weizhongli/cdhit","Cluster a nucleotide dataset into representative sequences.","shell","true","false"
"Centrifuge","1.0.3-conda","nucleic-acid-sequence-analysis","Microbiology,Metagenomics","https://ccb.jhu.edu/software/centrifuge/","A very rapid and memory-efficient system for the classification of DNA sequences from microbial samples. The system uses a novel indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini index, optimized specifically for the metagenomic classification problem. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers.","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"
"CheckM2","1.0.1-singularity","sequence-assembly-validation","Genomics","https://github.com/chklovski/CheckM2","Rapid assessment of genome bin quality using machine learning","singularity","false","false"
"CheckV","0.5.1-conda","sequence-assembly","Mapping,Sequence assembly,Metagenomics,Metagenomic sequencing","http://bitbucket.org/berkeleylab/CheckV","CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.","conda","false","false"
"chromeister","1.5.a-conda","dot-plot-plotting","Sequence analysis,Comparative genomics","https://github.com/estebanpw/chromeister","An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons (dotplot).","conda","true","false"
"chromonomer","1.14-bash","scaffolding","Mapping,Model organisms,Evolutionary biology,Sequence assembly,Genetics","http://catchenlab.life.illinois.edu/chromonomer","Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assembled according to the genetic map, and split those scaffolds.","bash","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","visualisation","Data visualisation,Comparative genomics","http://circos.ca/","Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well.","conda","false","false"
"Clair","2.1.1-conda","genome-assembly","Sequence assembly,Epigenetics,Machine learning,Genetic variation,Molecular biology","https://github.com/HKU-BAL/Clair","Exploring the limit of using a deep neural network on pileup data for germline variant calling.","conda","false","false"
"Clair3","0.1-r4.2-conda,0.1-conda","variant-calling","Molecular genetics","https://github.com/HKU-BAL/Clair3","Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.","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","DNA structural variation","https://github.com/etal/cnvkit","CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.","conda","false","false"
"Colony","2.0.6.8-shell","genetic-variation-analysis","Population genetics","https://www.zsl.org/science/software/colony","Implements a maximum likelihood method to assign sibship and parentage jointly, using individual multilocus genotypes at a number of codominant or dominant marker loci.","shell","false","false"
"Column Maker","1.6-conda","data-handling","Bioinformatics","https://github.com/galaxyproject/tools-iuc/blob/master/tools/column_maker/column_maker.xml","A Galaxy tool to compute an expression for every row of a dataset and appends the result as a new column","conda","true","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","virtual-ligand-screening","Protein-ligand interactions,Compound libraries and screening,Cheminformatics","https://github.com/UnixJunkie/consent","Ligand-based virtual screening with consensus queries.","shell","false","false"
"contig-extender","1.0-conda","de-novo-assembly,genome-assembly","Sequence assembly","https://github.com/dengzac/contig-extender","ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate contigs. ContigExtender is effective for extending contigs significantly in in silico synthesized and real metagenomics datasets.","conda","false","false"
"covtobed","1.3.5-conda","sequence-alignment-conversion","Sequence analysis","https://github.com/telatin/covtobed","Convert the coverage track from a BAM file into a BED file","conda","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","genetic-variation-analysis","Genetics,Genetic variation,Sequencing","https://bansal-lab.github.io/software/crisp.html","Identifies rare and common variants in pooled sequencing data","conda","false","false"
"Cufflinks","2.2.1-conda","standardisation-and-normalisation,rna-seq-read-count-analysis,gene-expression-comparison,aggregation,rna-seq-time-series-data-analysis,sequence-comparison","Transcriptomics,RNA splicing,RNA-Seq","http://cole-trapnell-lab.github.io/cufflinks","Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.","conda","false","false"
"CulebrONT","1.6-Snakemake,1.4-Snakemake","genome-assembly","Model organisms,Workflows,Sequence assembly","https://github.com/SouthGreenPlatform/CulebrONT_pipeline","CulebrONT is a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes.","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","4.1-conda,4.0-conda,2.8-conda,1.18-conda,1.16-conda,1.13-conda","sequence-trimming","Genomics,Probes and primers,Sequencing","https://pypi.python.org/pypi/cutadapt","Find and remove 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","variant-calling","Genetic variation,Metagenomics,Microbial ecology,Sequencing","http://bioconductor.org/packages/release/bioc/html/dada2.html","This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.","conda","false","false"
"DAS_Tool","1.1.4-conda,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","3.0.4-shell,2.0.6-shell","deposition,genome-annotation","Carbohydrates,Sequence sites, features and motifs,Metagenomics","http://cys.bios.niu.edu/dbCAN2/","Automated Carbohydrate-active enzyme ANnotation. Three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against the CAZy pre-annotated CAZyme sequence database and (iii) Hotpep search against the conserved CAZyme short peptide database.","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"
"dbOTU3","1.5.3-conda","community-profiling","Metagenomics","https://github.com/swo/dbotu3","Distribution-based OTU calling","conda","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"
"deepconsensus","0.2.0-singularity","base-calling","Sequence assembly","https://github.com/google/deepconsensus","DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data","singularity","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","base-calling","Methylated DNA immunoprecipitation,Epigenetics,DNA,Machine learning,Sequence sites, features and motifs","http://github.com/pepebonet/DeepMP","Deep learning tool to detect DNA base modifications on Nanopore sequencing data.","conda","false","false"
"DeepSignal-plant","0.1.5-conda,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","3.5.1-conda,3.4.3-conda","standardisation-and-normalisation","Genomics,ChIP-seq","https://deeptools.readthedocs.io/en/latest/","User-friendly tools for the normalization and visualization of deep-sequencing data.","conda","false","false"
"DeepVariant","1.1.0-singularity","variant-calling","DNA polymorphism,Exome sequencing,Genomics,Whole genome sequencing,Genotype and phenotype","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-alignment-analysis","Proteins,Sequence analysis","https://github.com/bbuchfink/diamond","Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.","singularity,conda,shell","false","false"
"DiscoSNP","2.4.4-conda","snp-detection","DNA polymorphism,Genetics,Genetic variation,Sequencing","https://colibread.inria.fr/software/discosnp/","This software is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).","conda","false","false"
"DRAP","1.91-docker","sequence-assembly-validation","Sequence analysis,Sequence assembly,RNA-seq","http://www.sigenae.org/drap/","De novo RNA-Seq Assembly Pipeline.","docker","false","false"
"drep","3.4.1-conda","genome-comparison","Genomics,Sequence analysis,Metagenomics","https://github.com/MrOlm/drep","Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.","conda","false","false"
"Dsuite","master-shell","genotyping","DNA polymorphism,Phylogenomics,Phylogeny","https://github.com/millanek/Dsuite","Fast calculation of the ABBA-BABA statistics across many populations/species.","shell","false","false"
"eCAMI","master-conda","database-search","Microbial ecology,Sequence sites, features and motifs,Plant biology,Enzymes,Small molecules","https://github.com/yinlabniu/eCAMI","simultaneous classification and motif identification for enzyme annotation.","conda","false","false"
"eggnog-mapper","2.1.8-conda,2.1.0-conda,1.0.3-conda","database-search","Genomics,Metagenomics","http://beta-eggnogdb.embl.de/#/app/emapper","For fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only. Its common uses include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.","conda","false","false"
"Eigensoft","7.2.1-conda","genetic-variation-analysis","Population genetics","https://www.hsph.harvard.edu/alkes-price/software/","Combindes functionality from population genetics methods (Patterson et al. 2006) and the EIGENSTRAT correection method (Price et al. 2006). The EIGENSTRAT methods uses principal component analysis to model ancestry differences between cases and controls along continuous axes of variation. The resulting correction is specific to a candidate markers variation in frequency across ancestral populations, minimizing spurious associations while maximising power to detect true associations.","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"
"emblmygff3","2.2-conda","formatting","Data submission, annotation and curation","https://github.com/NBISweden/EMBLmyGFF3","Software to convert GFF3 and fasta to legal EMBL format suitable for ENA submission.","conda","false","false"
"EMBOSS","6.5.7-conda","sequence-analysis","Biology,Sequence analysis,Molecular biology","http://emboss.bioinformatics.nl/","Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.","conda","false","false"
"ena-bulk-webincli","1.0.0-singularity","deposition","Data management","https://github.com/enasequence/ena-bulk-webincli","ENA Webin-CLI Bulk Submission Tool : this tool is a wrapper to bulk submit read, un-annotated genome, targeted sequence or taxonomic reference data to the ENA using Webin-CLI.","singularity","false","false"
"ena-webin-cli","6.3.0-singularity,5.1.0-conda","deposition","Data management","https://github.com/enasequence/webin-cli","Data submissions to ENA can be made using the Webin command line submission interface (Webin-CLI). Webin submission account credentials are required to use the program.","singularity,conda","false","false"
"ensembl-vep","106.1-conda,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"
"est-sfs","2.03-shell","statistics-and-probability","Population genetics","https://sourceforge.net/projects/est-usfs/","Etimation of the unfolded site frequency spectrum","shell","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"
"Fasta Statistics","2.0-conda","validation","Bioinformatics","https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/","Display summary statistics for a fasta file.","conda","true","false"
"FastANI","1.3-conda","genome-alignment","Microbiology,Genetic variation","https://github.com/ParBLiSS/FastANI","FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.","conda","true","false"
"fastp","0.23.2-conda,0.20.1-conda,0.20.0-conda,0.19.5-conda","sequence-trimming","Sequence analysis,Probes and primers","https://github.com/OpenGene/fastp","A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.","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","sequence-composition-calculation","Sequence analysis,Data quality management,Sequencing","http://www.bioinformatics.babraham.ac.uk/projects/fastqc/","This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.","conda","true","false"
"","0.2.6-conda","","","","","conda","true","false"
"fastsimcoal2","fsc2603-shell","genotyping","DNA polymorphism,Gene transcripts,Genotype and phenotype,Mapping","http://cmpg.unibe.ch/software/fastsimcoal2/","Fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework.","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","read-pre-processing","Sequence analysis","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 sites, features and motifs,Sequence assembly,Metagenomics","https://github.com/Arkadiy-Garber/FeGenie","a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies | HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes | Please see the Wiki page for introduction and tutorial on how to use this tool | git clone https://github.com/Arkadiy-Garber/FeGenie.git | Easy Installation (if you have Conda installed) | HMM-lib directory can be found within FeGenie's main repository -t 8 means that 8 threads will be used for HMMER and BLAST. If you have less than 16 available on your system, set this number lower (default = 1)","conda","false","false"
"FIGARO","1.1.2-singularity","data-handling","Metagenomics","https://github.com/Zymo-Research/figaro","An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters","singularity","false","false"
"FigTree","1.4.4-conda","phylogenetic-tree-visualisation","Phylogenetics,Data visualisation","http://tree.bio.ed.ac.uk/software/figtree/","This tool is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.","conda","false","false"
"Fiji","20170530-conda","quantification","Cell biology,Imaging","https://fiji.sc","A quantitative method to analyse F-actin distribution in cells.","conda","false","false"
"FImpute","2.2-shell","imputation","Population genetics","http://www.aps.uoguelph.ca/~msargol/fimpute/","Developed for large scale genotype imputation in livestock where hundreds of thousands of individuals are genotypes with different panels. It uses an overlapping sliding window approach to exploit relationships or haplotype similarities between target and reference individuals. The process starts with long windows to capture haplotype similarity between close 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","read-pre-processing","Sequence assembly,Sequencing","http://ccb.jhu.edu/software/FLASH/","Identifies paired-end reads which overlap in the middle, converting them to single long 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","2.9.1-conda,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","Whole genome sequencing,Sequence assembly,Metagenomics","https://github.com/fenderglass/Flye","Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.","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","Proteins,Structure prediction,Protein folds and structural domains,Genetic variation,Protein folding, stability and design","http://foldxsuite.crg.eu/","FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.","conda","false","false"
"FragGeneScan","1.31-conda","gene-prediction","Genetics,Sequence analysis","https://sourceforge.net/projects/fraggenescan/","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","Rare diseases,Genomics,Genetic variation","https://github.com/ekg/freebayes","Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.","conda","true","false"
"FROGS","4.0.1-conda,3.2.1-conda,2.0.0-conda,1.4.0-conda","taxonomic-classification","Evolutionary biology,Sequencing,Microbial ecology,Taxonomy,Metagenomics","http://frogs.toulouse.inra.fr/","The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.","conda","false","false"
"funannotate","1.8.9-conda,1.8.7-conda,1.8.12-singularity,1.8.11-conda","genome-annotation","Genomics","https://github.com/nextgenusfs/funannotate","funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).","conda,singularity","true","false"
"galba","1.0.0-singularity","genome-annotation","Gene transcripts,Genomics,Workflows","https://github.com/Gaius-Augustus/GALBA","GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from a closely related species are available.","singularity","false","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","Endocrinology and metabolism,Microbial ecology,Genotype and phenotype,Enzymes,Molecular interactions, pathways and networks","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","polymorphism-detection","Workflows,Genetic variation,Sequence analysis,Sequencing","https://software.broadinstitute.org/gatk/","The Genome Analysis Toolkit (GATK) is a set of bioinformatic tools for analyzing high-throughput sequencing (HTS) and variant call format (VCF) data. The toolkit is well established for germline short variant discovery from whole genome and exome sequencing data. GATK4 expands functionality into copy number and somatic analyses and offers pipeline scripts for workflows.  ","conda","false","false"
"Gblocks","0.91b-conda","sequence-alignment-analysis","Sequence analysis","http://www.embl-heidelberg.de/~castresa/Gblocks/Gblocks.html","Cleaning aligned sequences.","conda","true","false"
"gemBS","3.5.5-conda","whole-genome-methylation-analysis","Epigenetics","https://github.com/heathsc/gemBS","A high performance bioinformatic pipeline designed for highthroughput analysis of DNA methylation data from whole genome bisulfites sequencing data (WGBS).","conda","false","false"
"Gemma","0.98.5-shell","differential-gene-expression-analysis","Genomics,Genetics,Gene expression","http://chibi.ubc.ca/Gemma","Gemma is an open source database, analysis software system and web site for expression data re-use and meta-analysis. It currently contains analyzed data from over 3300 expression profiling studies, yielding billions of data points that can be searched and explored. Gemma offers web-based access to differential expression results and coexpression data in a meta-analysis framework.","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","Gene structure","http://exon.gatech.edu/GeneMark/","A family of gene prediction programs: Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes; Gene Prediction in Eukaryotes; Gene Prediction in Transcripts; Gene Prediction in Viruses, Phages and Plasmids.","conda","false","false"
"GeneMarkS-T","5.1-conda","sequence-assembly","Model organisms,Sequence assembly,Gene expression","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"
"genomad","1.5.1-conda,1.5.0-conda","sequence-annotation","Sequence analysis","https://portal.nersc.gov/genomad/","geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.","conda","false","false"
"genomescope2","2.0-conda","sequence-assembly","Sequence assembly","https://github.com/tbenavi1/genomescope2.0","Reference-free profiling of polyploid genomes","conda","true","false"
"GenomeThreader","1.7.3-shell","sequence-feature-detection","Gene structure,Structure prediction","http://genomethreader.org/","Software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments.","shell","false","false"
"genometools","1.6.1-conda","sequence-analysis","Sequence analysis,Nucleic acid sites, features and motifs","http://genometools.org/","Free collection of bioinformatics tools for genome informatics.","conda","false","false"
"GetOrganelle","1.7.5.0-conda","de-novo-assembly","Sequence assembly,Model organisms,Whole genome sequencing,Plant biology,Cell biology","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"
"GFA to FASTA","0.1.2-shell","data-handling","Sequence assembly","http://gfa-spec.github.io/GFA-spec/","Converting GFA format to Fasta format","shell","true","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","Nucleic acids,Sequence analysis","https://ccb.jhu.edu/software/stringtie/gff.shtml","Program for comparing, annotating, merging and tracking transcripts in GFF files.","conda","false","false"
"gffread","0.12.7-conda","sequence-annotation","Nucleic acids,Sequence analysis","https://ccb.jhu.edu/software/stringtie/gff.shtml","program for filtering, converting and manipulating GFF files","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 analysis,Sequence assembly,DNA,Sequencing","http://sourceforge.net/projects/gmcloser/","Fill and close the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads.","docker","false","false"
"gmove","b0b2ada-singularity","gene-prediction","RNA-Seq,Genomics","http://www.genoscope.cns.fr/gmove","Gmove is a genome annotation tool. This combiner takes as input mapping of RNA-seq or protein or ab initio data.","singularity","false","false"
"Gnuplot","5.4.2-shell","data-visualisation","Data visualisation","http://www.gnuplot.info/","a portable command-line driven graphing utility.","shell","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. It is available in Galaxy Europe and as a stand-alone tool.","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"
"goseq","1.44.0-conda","gene-functional-annotation","RNA-seq","http://bioconductor.org/packages/release/bioc/html/goseq.html","Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.","conda","true","false"
"goslimmer","1.0-conda","gene-set-enrichment-analysis","Transcriptomics","https://github.com/DanFaria/GOEnrichment","GOSlimmer transforms GO Annotations to slimmed versions of GO (GOSlimmer tool from the goenrichment package )","conda","true","false"
"gowinda","1.12-docker","gene-set-enrichment-analysis","Population genetics,Genomics,Population genomics,Sequencing","http://code.google.com/p/gowinda/","Gowinda: unbiased analysis of gene set enrichment for Genome Wide Association Studies","docker","false","false"
"GraphBin","1.3-conda,1.1-conda","sequence-assembly","Mapping,Sequence assembly,Sequencing,Microbial ecology,Metagenomics","https://github.com/Vini2/GraphBin","Refined binning of metagenomic contigs using assembly graphs.","conda","false","false"
"GSAlign","1.0.22-conda","genome-indexing","Structure analysis,Genomics,Sequence analysis,Sequencing","https://github.com/hsinnan75/GSAlign","An efficient sequence alignment tool for intra-species genomes.","conda","false","false"
"Collapse Collection","5.1.0-conda","data-handling","Bioinformatics","https://toolshed.g2.bx.psu.edu/repository?repository_id=7bd57763926b9cbf","Collection tool that collapses a list of files into a single datasset in order of appears in collection","conda","true","false"
"Collection Elements Identifiers","0.0.2-shell","data-handling","Bioinformatics","https://github.com/galaxyproject/tools-iuc/blob/master/tools/collection_element_identifiers/collection_element_identifiers.xml","Extract element identifiers of a collection","shell","true","false"
"Column Maker","2.0-conda","data-handling","Bioinformatics","https://github.com/galaxyproject/tools-iuc/blob/master/tools/column_maker/column_maker.xml","A Galaxy tool to compute an expression for every row of a dataset and appends the result as a new column","conda","true","false"
"Deg Annotate","1.0-conda","differential-gene-expression-analysis","Transcriptomics","https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate","This tool appends the output table of DESeq2/edgeR/limma/DEXSeq with gene symbols, biotypes, positions etc","conda","true","false"
"Filter sequences by length","1.2-conda","data-handling","Bioinformatics","https://github.com/galaxyproject/tools-devteam/blob/main/tools/fasta_filter_by_length/fasta_filter_by_length.xml","Outputs sequences between Minimal length and Maximum length","conda","true","false"
"Gene length and GC content","0.1.2-conda","data-handling","Bioinformatics","https://github.com/galaxyproject/tools-iuc/blob/master/tools/length_and_gc_content","This galaxy tool calculates the length and/or GC content for the genes in a GTF file","conda","true","false"
"Table Compute","1.2.4-conda","data-handling","Bioinformatics","","A Galaxy wrapper to perform general-purpose table operations","conda","true","false"
"Galaxy Text Manipulation","1.0-shell","editing","Bioinformatics","https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing","Galaxy wrappers for common unix text-processing tools","shell","true","false"
"GTDB-Tk","2.1.0-conda,2.0.0-conda,1.5.0-conda,1.4.1-conda,1.1.0-conda,1.0.2-conda","genome-alignment","Database management,Proteins,Phylogenetics,Taxonomy,Metagenomics","https://github.com/ecogenomics/gtdbtk","a toolkit to classify genomes with the Genome Taxonomy Database.","conda","false","false"
"Convert GTF to BED12","357-conda","data-handling","Bioinformatics","http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README","Convert GTF files to BED12 format using the UCSC Kent Bioinformatics utiltities","conda","true","false"
"gubbins","3.3-conda","genotyping","Whole genome sequencing,Genotype and phenotype,Phylogeny","https://github.com/sanger-pathogens/gubbins","Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.","conda","false","false"
"guppy","6.4.2-bash,4.5.3-shell,3.6.0-shell","sequence-visualisation","Genomics,Genetics,Data visualisation,Sequencing","http://staff.aist.go.jp/yutaka.ueno/guppy/","Program to visualize sequence annotation data of the genetic sequence data with graphical layout. This highly interactive program allows scrolling and zooming from the genomic landscape to discrete nucleic acid sequences. Its main function is quick rendering of data on a standalone personal computer to save the layout as a parsonal file. With optional link to the internet resources, and printing support, this program tries to make more greater use of computational media in research actitiviy.","bash,shell","false","false"
"hap.py","v0.3.12-singularity","variant-calling","DNA polymorphism,Genomics","https://github.com/Illumina/hap.py","This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.","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","sequence-feature-detection,genotyping","Population genetics,Genetics,Genotype and phenotype,Genotyping experiment","https://forge-dga.jouy.inra.fr/projects/hapflk","Software for the detection of selection signatures based on multiple population genotyping data.","conda","false","false"
"Haploclique","1.3.1-conda","sequence-assembly","Genetics,Virology,Sequencing","https://github.com/cbg-ethz/haploclique","Computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.","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"
"hapog","1.3.2-conda","genome-assembly","Genomics,Sequence assembly","https://github.com/institut-de-genomique/HAPO-G","Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.","conda","false","false"
"HASLR","0.8a1-conda","genome-assembly","Mapping,Sequence assembly,Sequencing","https://github.com/vpc-ccg/haslr","Fast Hybrid Assembly of Long Reads.","conda","false","false"
"helixer","0.3.0-singularity","gene-prediction","Gene transcripts,Sequence analysis","https://github.com/weberlab-hhu/Helixer","Deep Learning to predict gene annotations","singularity","false","false"
"HHsuite","3.0-beta.3-shell","sequence-analysis","Proteins","https://github.com/soedinglab/hh-suite","HH-suite is a remote protein homology detection suite.","shell","false","false"
"hifiasm-meta","0.3.1-conda","sequence-assembly","Metagenomics,Sequence assembly","https://github.com/xfengnefx/hifiasm-meta","Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.","conda","false","false"
"hifiasm","0.18.9-bash,0.18.5-bash,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: a haplotype-resolved assembler for accurate Hifi reads","bash,shell,conda","false","false"
"hiline","0.2.4-conda","read-mapping","Mapping,Epigenetics","https://github.com/wtsi-hpag/HiLine","HiC alignment and classification pipeline","conda","false","false"
"HISAT2","2.2.1-conda,2.1.0-conda,2.0.5-conda","sequence-alignment","RNA-seq","https://ccb.jhu.edu/software/hisat2/index.shtml","Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).","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","sequence-assembly","Model organisms,Sequence assembly,Machine learning,Metagenomics","https://github.com/ythuang0522/homopolish","Homopolish is a method for the removal of systematic errors in nanopore sequencing by homologous polishing.","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","1.3.3-conda,1.2.0-conda","sequence-trimming","Genomics,Sequence analysis,Data quality management,Probes and primers","https://s4hts.github.io/HTStream/","HTStream is a quality control and processing pipeline for High Throughput Sequencing data. The difference between HTStream and other tools is that HTStream uses a tab delimited fastq format that allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data and makes it fully interoperable with other standard Linux tools.","conda","false","false"
"HyPhy","2.3.14-conda","statistical-calculation","Small molecules,Phylogeny,Molecular interactions, pathways and networks","http://hyphy.org","Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.","conda","false","false"
"IDBA","1.1.3-conda","sequence-assembly","Sequence assembly","http://i.cs.hku.hk/%7Ealse/idba","A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.","conda","false","false"
"IGV","2.8.10-conda,2.5.3-shell","visualisation,sequence-assembly-visualisation","Genomics,Sequence analysis,Data visualisation","http://www.broadinstitute.org/igv/","High-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or over the web via http.","conda,shell","false","false"
"igvtools","2.5.3-conda","formatting","Sequence analysis","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","nucleic-acid-feature-detection","Sequence sites, features and motifs","http://eddylab.org/infernal/","Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.","conda","false","false"
"instaGRAAL","0.1.2-shell","genome-assembly","Mapping,Sequence assembly,Statistics and probability,DNA binding sites,Metagenomics","https://github.com/koszullab/instaGRAAL","Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.","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","2.2.0_beta-conda","phylogenetic-tree-generation-(maximum-likelihood-and-bayesian-methods)","Phylogenetics,Phylogenomics,Statistics and probability","http://www.cibiv.at/software/iqtree/","Very efficient phylogenetic software for reconstructing maximum-likelihood trees and assessing branch supports with the ultrafast bootstrap approximation. It is based on the IQPNNI algorithm with 10-fold speedup together with substantially additional features.","conda","false","false"
"iq-tree","2.0.3-conda,1.6.7-conda,1.5.5.1-conda","phylogenetic-tree-generation-(maximum-likelihood-and-bayesian-methods)","Phylogenetics,Phylogenomics,Statistics and probability","http://www.cibiv.at/software/iqtree/","Very efficient phylogenetic software for reconstructing maximum-likelihood trees and assessing branch supports with the ultrafast bootstrap approximation. It is based on the IQPNNI algorithm with 10-fold speedup together with substantially additional features.","conda","true","false"
"isoseq3","3.4.0-conda","demultiplexing","Gene transcripts","https://github.com/PacificBiosciences/IsoSeq","IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique.","conda","false","false"
"ivar","1.2.2-conda","variant-classification","Evolutionary biology,Biological databases,Sequencing","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","Genomics","http://gmod.org/wiki/JBrowse","Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.","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","2.3.0-conda,2.2.6-conda,2.2.10-conda","k-mer-counting","Genomics,Sequence analysis","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","1.9.0-conda,1.8.2-conda,1.7.3-conda,1.7.1-conda","taxonomic-classification","Metagenomics","http://kaiju.binf.ku.dk","Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses.","conda","false","false"
"Kalign","2.04-shell","multiple-sequence-alignment","Sequence analysis","http://www.ebi.ac.uk/Tools/msa/kalign/","Fast and accurate multiple sequence alignment which handles large sequences.","shell","false","false"
"kallisto","0.48.0-conda,0.46.2-conda","gene-expression-profiling","Transcriptomics,Gene expression,RNA-seq","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. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.","conda","false","false"
"kat","2.4.2-conda","sequence-composition-calculation","Genomics,Sequence analysis","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","variant-calling","RNA-Seq,Genetic variation,Transcriptomics","http://kissplice.prabi.fr","KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome.","conda","false","false"
"KMC","3.2.1-conda,3.1.2rc1-conda","k-mer-counting","Genomics,Whole genome sequencing,Sequence assembly","http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about","KMC is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.","conda","false","false"
"KmerGenie","1.7016-conda","sequence-assembly","Sequence assembly","http://kmergenie.bx.psu.edu/","KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie's choices lead to assemblies that are close to the best possible over all k-mer lengths.","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"
"kraken","1.1.1-conda","taxonomic-classification","Metagenomics,Taxonomy","https://ccb.jhu.edu/software/kraken/","System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.","conda","false","false"
"Kraken2","2.1.2-conda,2.1.1-conda,2.0.9beta-conda","taxonomic-classification","Metagenomics,Taxonomy","https://ccb.jhu.edu/software/kraken2/","Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.","conda","false","false"
"KrakenUniq","1.0.2-conda,0.7.3-conda,0.5.8-conda","quantification","Metagenomic sequencing,Infectious disease,Whole genome sequencing,Taxonomy,Metagenomics","https://github.com/hurwitzlab/krakenuniq","Identification and quantitation of clinically relevant microbes in patient samples.","conda","false","false"
"Krona","2.8.1-conda,2.7-conda","visualisation","Metagenomics","https://github.com/marbl/Krona/wiki","Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).","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","0.5-bash,0.2-shell","mapping","Mapping","https://sourceforge.net/projects/lep-map3/","Robust linkage mapping software even for low coverage whole genome sequencing data","bash,shell","false","false"
"LINKS","1.8.6-shell","scaffolding","Mapping,Sequence assembly,Sequencing","https://github.com/bcgsc/LINKS","LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.","shell","false","false"
"lofreq","2.1.5-conda","variant-calling","Genomics,Genetic variation","https://csb5.github.io/lofreq/","LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.","conda","false","false"
"longshot","0.4.3-singularity,0.4.2-singularity,0.4.1-conda","variant-calling","Genetic variation","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). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also genotype and phase input VCF files. It can output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs), but it can genotype indels if they are given in an input VCF.","singularity,conda","false","false"
"LRA","1.3.2-conda","read-mapping","Whole genome sequencing,Structure analysis,Sequence assembly,Bioinformatics","https://anaconda.org/bioconda/lra","the Long Read Aligner for Sequences and Contigs.","conda","false","false"
"LRBinner","0.1-conda","read-binning","Sequence assembly,Metagenomic sequencing,Machine learning,Sample collections,Metagenomics","https://github.com/anuradhawick/LRBinner","Binning long reads in metagenomics datasets using composition and coverage information.","conda","false","false"
"lulu","0.1-conda","rarefaction","Biodiversity,Metagenomics,Sequencing","https://github.com/tobiasgf/lulu","A flexible pipeline combining bioinformatic correction tools for prokaryotic and eukaryotic metabarcoding | r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding) | The purpose of LULU is to reduce the number of erroneous OTUs in OTU tables to achieve more realistic biodiversity metrics. By evaluating the co-occurence patterns of OTUs among samples LULU identifies OTUs that consistently satisfy some user selected criteria for being errors of more abundant OTUs and merges these. It has been shown that curation with LULU consistently result in more realistic diversity metrics. The required input of LULU is an OTU table and a corresponding matchlist with all the internal matches of OTUs | A r-package for distribution based post clustering curation of amplicon data","conda","false","false"
"MACS","2.1.1.20160309-conda","peak-calling","Transcription factors and regulatory sites,ChIP-seq,Molecular interactions, pathways and networks","http://liulab.dfci.harvard.edu/MACS/","Model-based Analysis of ChIP-seq data.","conda","true","false"
"MACSE","2.01-conda","multiple-sequence-alignment","Molecular evolution,Structure analysis,Protein expression,Phylogenomics,Gene transcripts","https://bioweb.supagro.inra.fr/macse/","Aligning Protein-Coding Nucleotide Sequences with MACSE.","conda","false","false"
"MAFFT","7.490-conda,7.310-conda,7.245-conda","multiple-sequence-alignment","Sequence analysis","http://mafft.cbrc.jp/alignment/server/index.html","MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.","conda","true","false"
"mamba","1.3.0-conda,1.2.0-conda,1.0.0-conda,0.25.0-conda,0.24.2-conda,0.21.2-conda,0.19.0-conda","forcefield-parameterisation","Machine learning,Chemistry,Small molecules,Cheminformatics","https://github.com/CHLoschen/mamba","Perception of Chemical Bonds via Machine Learning.","conda","false","false"
"marginPhase","1.0.0-singularity","haplotype-mapping","Genotype and phenotype","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","DNA mutation,Sequence analysis,Genomics,Statistics and probability,Metagenomics","https://github.com/marbl/mash","Fast genome and metagenome distance estimation using MinHash.","shell","true","false"
"masurca","4.0.9-conda","genome-assembly","Whole genome sequencing,Sequence assembly,Sequence analysis","http://www.genome.umd.edu/masurca.html","Whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).","conda","true","false"
"mauve-viewer","1.0.0-beta-conda","genome-alignment","Data visualisation","https://github.com/PATRIC3/mauve-viewer","A JavaScript Mauve/.xmfa viewer for multiple whole genome alignments.","conda","false","false"
"Mauve","2.4-conda","sequence-alignment-comparison","Genomics,Transcriptomics","http://darlinglab.org/mauve","Mauve Genome Alignment software, for comparing two or more draft or finished genomes","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","1.7.2-singularity,1.4.3-conda,1.3.3-conda,1.2.6-conda,0.11.4-conda","base-calling","Machine learning,Sequence assembly","https://github.com/nanoporetech/medaka","medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.","singularity,conda","false","false"
"MEGAHIT","1.1.1-conda","genome-assembly","Ecology,Sequence assembly,Metagenomics,Sequencing","https://github.com/voutcn/megahit","Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.","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"
"merqury","1.3-conda","genome-assembly","Whole genome sequencing,Sequence assembly,Plant biology","https://github.com/marbl/merqury","Reference-free quality, completeness, and phasing assessment for genome assemblies.","conda","true","false"
"meryl","1.3-conda","k-mer-counting","Genomics,Whole genome sequencing,Sequence analysis","https://github.com/marbl/meryl","Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.","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"
"MetaBCC-LR","2.0.0-conda","read-binning","Sequencing,Sequence assembly,Metagenomics,Microbial ecology","https://github.com/anuradhawick/MetaBCC-LR","Metagenomics binning by coverage and composition for long reads.","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"
"MetaEuk","5.34c21f2-conda","homology-based-gene-prediction","Gene and protein families,Metagenomics","https://metaeuk.soedinglab.org/","MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics","conda","false","false"
"MetaPhage","0.3.0-Nextflow","sequence-annotation","Genomics,Workflows","https://mattiapandolfovr.github.io/MetaPhage/","a nextflow pipeline for automatic phage discovery","Nextflow","false","false"
"Metapop","0.0.60-conda","genotyping","DNA polymorphism,Population genetics,Genotype and phenotype","https://quercusportal.pierroton.inra.fr/index.php?p=METAPOP","Individual-based model for simulating the evolution of tree populations in spatially and temporally heterogeneous landscapes.","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","bisulfite-mapping","Epigenetics,Sequencing","http://smithlabresearch.org/software/methpipe/","The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS). MethPipe provides tools for mapping bisulfite sequencing read and estimating methylation levels at individual cytosine sites. Additionally, MethPipe includes tools for identifying higher-level methylation features, such as hypo-methylated regions (HMR), partially methylated domains (PMD), hyper-methylated regions (HyperMR), and allele-specific methylated regions (AMR).","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","sequence-alignment-conversion","Epigenomics","https://github.com/dpryan79/MethylDackel","A (mostly) universal methylation extractor for BS-seq experiments.","conda","false","false"
"MethylExtract","1.9.1-docker","methylation-analysis","Epigenetics,DNA,Sequencing","http://bioinfo2.ugr.es/MethylExtract/","User friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation.","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"
"MGKit","0.5.0-conda","workflows","Metagenomics","https://mgkit.readthedocs.io/en/0.5.0/introduction.html","The aim of MGKit is to provide a series of useful modules and packages to make it easier to build custom pipelines for metagenomics or any kind of bioinformatics analysis.","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","de-novo-assembly","Genomics,Sequence assembly","https://github.com/lh3/miniasm","Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.","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","pairwise-sequence-alignment","Mapping","https://github.com/lh3/minimap2","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"
"miniprot","0.7-conda,0.6-conda,0.5-conda,0.3-conda","sequence-alignment","Sequence analysis,Sequence sites, features and motifs","https://github.com/lh3/miniprot","Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.","conda","false","false"
"MIRA","4.9.6-conda","local-alignment","Sequence assembly,RNA-Seq","https://sourceforge.net/p/mira-assembler/wiki/Home/","MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler","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"
"mitohifi","2.2-singularity","genome-assembly","Genomics,Sequence analysis,Sequence assembly","https://github.com/marcelauliano/MitoHiFi","Find, circularise and annotate mitogenome from PacBio assemblies","singularity","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","Immunoproteins, genes and antigens","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,14.7e284-conda,11.e1a1c-conda","taxonomic-classification,sequence-similarity-search,sequence-clustering","Nucleic acids,Proteins,Sequence analysis,Taxonomy,Gene and protein families,Metagenomics","https://mmseqs.com","MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.","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","Phylogenetics,Computer science,Small molecules","https://github.com/ddarriba/modeltest","A new and scalable tool for the selection of DNA and protein evolutionary models | ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces","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"
"mosdepth","0.2.7-conda","nucleic-acid-sequence-analysis","Data quality management,Statistics and probability","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","","Microbial ecology","http://mothur.org/","Open-source, platform-independent, community-supported software for describing and comparing microbial communities","conda","false","false"
"MrBayes","3.2.7-conda","phylogenetic-tree-generation-(maximum-likelihood-and-bayesian-methods)","Phylogenetics","http://nbisweden.github.io/MrBayes/","Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.","conda","true","false"
"MrBayes","3.2.6-conda","phylogenetic-tree-generation-(maximum-likelihood-and-bayesian-methods)","Phylogenetics","http://nbisweden.github.io/MrBayes/","Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.","conda","true","false"
"msamtools","1.1.0-conda","data-handling","Metagenomics","https://github.com/arumugamlab/msamtools","microbiome-related extension to samtools","conda","false","false"
"MultiNanopolish","master-conda","sequence-assembly","DNA polymorphism,Sequence sites, features and motifs,Sequence assembly","https://github.com/BioinformaticsCSU/MultiNanopolish","Refined grouping method for reducing redundant calculations in nanopolish.","conda","false","false"
"multiqc","1.14-conda,1.13-conda,1.12-conda,1.11-conda","validation","Bioinformatics,Sequencing","http://multiqc.info/","MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.","conda","true","false"
"MUMmer","4.0.0rc1-conda,4.0.0beta2-conda,3.23-conda","sequence-alignment","Genomics,Mapping,Sequencing","http://mummer.sourceforge.net/","MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Basically it is a ultra-fast alignment of large-scale DNA and protein sequences","conda","false","false"
"mumu","1.0.0-singularity","sequence-clustering","Metagenomics","https://github.com/frederic-mahe/mumu","fast and robust C++ implementation of lulu, a R package for post-clustering curation of metabarcoding data","singularity","false","false"
"muscle","3.8-conda","multiple-sequence-alignment","Sequence analysis","https://www.drive5.com/muscle/","This tool performs multiple sequence alignments of nucleotide or amino acid sequences.","conda","false","false"
"n50","1.4.2-conda","statistical-calculation","Bioinformatics","https://metacpan.org/release/Proch-N50","A script to calculate N50 from one or multiple FASTA/FASTQ files available via BioConda","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","indel-detection","DNA polymorphism,Mapping,Machine learning,Sequencing","https://github.com/WGLab/NanoCaller","NanoCaller for accurate detection of SNPs and small indels from long-read sequencing by deep neural networks.","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","scatter-plot-plotting","Genomics","https://github.com/wdecoster/NanoPlot","NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences","conda","true","false"
"Nanopolish","0.13.2-conda","statistical-calculation","Genetic variation,Sequence analysis,Statistics and probability,Sequencing","https://github.com/jts/nanopolish","A package for detecting cytosine methylations and genetic variations from nanopore MinION sequencing data.","conda","false","false"
"ncbi-datasets-cli","13.29.1-conda,13.10.0-conda","data-handling","Biological databases","https://github.com/ncbi/datasets","NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.","conda","false","false"
"ncbi-datasets-pylib","13.10.0-conda,10.2.0-conda","data-handling","Bioinformatics","https://pypi.org/project/ncbi-datasets-pylib/","Easily gather data from across NCBI databases","conda","false","false"
"ncbi-datasets","14.3.0-conda,14.14.0-conda,14.0.0-conda","data-handling","Biological databases","https://github.com/ncbi/datasets","NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.","conda","false","false"
"ncbi_fcs","0.2.2-singularity","sequence-assembly-validation","Sequence analysis,Sequence assembly","https://github.com/ncbi/fcs","The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.","singularity","false","false"
"NextDenovo","2.4.0-singularity","de-novo-assembly","Sequence assembly","https://github.com/Nextomics/NextDenovo","NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.","singularity","false","false"
"Nextflow","22.10.4-conda,22.10.0-conda,22.04.0-conda,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","service-composition","Genomics,Bioinformatics,Workflows,Software engineering","https://www.nextflow.io/","Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.","conda","false","false"
"NF-CORE","2.6-conda,2.5.1-conda,1.9-conda","workflows","Bioinformatics","https://nf-co.re/tools","Nextflow community tools","conda","false","false"
"ngmlr","0.2.7-conda","genetic-variation-analysis","Mapping","https://github.com/philres/ngmlr","An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.","conda","false","false"
"NGSUtils","0.5.9-conda","read-pre-processing","Genomics,Transcriptomics","http://ngsutils.org","NGSUtils is a suite of software tools for working with next-generation sequencing datasets","conda","false","false"
"npScarf","2019.09-conda","genome-assembly","Sequence assembly,Sequencing","https://github.com/mdcao/npScarf","A hybrid sequence assembler that can scaffold and complete fragmented short read assemblies with sequence data streaming from the nanopore sequencing while sequencing is still in progress. Furthermore, it continuously reports assembly quality during the experiment so that users can terminate the sequencing when an assembly of sufficient quality and completeness is obtained.","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","sequence-analysis","Sequence analysis,DNA,Sequencing","https://git.metabarcoding.org/obitools/obitools/wikis/home","Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.","singularity","false","false"
"Octopus","0.7.4-conda,0.6.3b-conda","transmembrane-protein-analysis","Sequence analysis","http://octopus.cbr.su.se/","Prediction of membrane protein topology and signal peptides.","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"
"omegaplus","3.0.3-shell","genetic-variation-analysis","Population genetics","https://github.com/alachins/omegaplus","HPC population genetics code for selective sweep detection","shell","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/","Scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, out-performing state-of-the-art programs for scaffold correctness and contiguity. It provides a rigorous framework for scaffolding of repetitive sequences and a systematic approach for combining data from different second-generation and third-generation sequencing technologies.","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","2.5.4-conda,2.4.0-conda","genome-comparison","Sequence analysis,Comparative genomics,Phylogenetics,Phylogenomics,Bioinformatics","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. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.","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"
"pathview","1.24.0-conda","pathway-or-network-analysis","Systems biology,Data visualisation,Molecular interactions, pathways and networks","http://bioconductor.org/packages/release/bioc/html/pathview.html","Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.","conda","true","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. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.","conda","false","false"
"PCAdapt","3.0.4-conda","sequence-analysis","Genomics,Population genetics,Genetics,Evolutionary biology","http://membres-timc.imag.fr/Nicolas.Duforet-Frebourg/PCAdapt.html","Software to detect footprints of local adaptation in population genetics data set.","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","sequence-merging","Sequence assembly","http://sco.h-its.org/exelixis/web/software/pear/","Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.","conda","false","false"
"pecheck","0.2.0-shell","data-handling","Bioinformatics","https://github.com/OpenGene/pecheck","A tool to check paired-end FASTQ data integrity","shell","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-bootstrapping","Phylogeny,Phylogenetics,Model organisms,Physiology,Gene and protein families","http://evolution.genetics.washington.edu/phylip.html","Comprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX.","conda","true","false"
"phyloFlash","3.4-conda","sequence-assembly","Sequence assembly,Microbial ecology,Metatranscriptomics,Functional, regulatory and non-coding RNA,Metagenomics","https://github.com/HRGV/phyloFlash","Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes.","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-generation-(maximum-likelihood-and-bayesian-methods)","Phylogenetics,Bioinformatics","http://www.atgc-montpellier.fr/phyml/","Phylogenetic estimation software using Maximum Likelihood","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","true","false"
"PICRUSt","1.1.0-conda","phylogenetic-reconstruction","Functional, regulatory and non-coding RNA,Metagenomic sequencing,Metagenomics,Microbial ecology","http://picrust.github.io/picrust/","PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.","conda","false","false"
"PICRUSt2","2.5.1-conda,2.4.2-conda","pathway-analysis","Metagenomics","https://github.com/picrust/picrust2","PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.","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","sequence-assembly,read-alignment,analysis","Assembly","http://www.broadinstitute.org/software/pilon/","Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.","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","Transcriptomics,Sequence assembly,Metagenomics","https://plass.mmseqs.com","Protein-Level ASSembler (PLASS): sensitive and precise protein assembler","conda","false","false"
"PLAST","2.3.3-shell,2.3.2-shell","local-alignment","Sequence analysis","http://www.irisa.fr/symbiose/projects/plast/","Parallel Local Alignment Search Tool for Database Comparison.","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","sequence-classification","Mobile genetic elements","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/","Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.","shell","true","false"
"Plotsr","0.5.3-conda","structure-visualisation","DNA polymorphism,Mapping,Sequence assembly","https://github.com/schneebergerlab/plotsr","Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies.","conda","false","false"
"PointFinder","2018-05-23-conda","polymorphism-detection","GWAS study,DNA,Whole genome sequencing,Bioinformatics,Genetic variation","http://bitbucket.org/genomicepidemiology/pointfinder_db","PointFinder is an Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites.","conda","false","false"
"polypolish","0.5.0-conda","genome-assembly","Sequence composition, complexity and repeats,Sequence assembly,Mapping","https://github.com/rrwick/Polypolish","Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.","conda","true","false"
"PoPoolation2","1201-docker","sequence-feature-comparison","DNA polymorphism,Population genetics,Genomics","https://sourceforge.net/projects/popoolation2/","PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution.","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"
"porechop_ABI","0.5.0-conda","sequence-trimming,demultiplexing","Genomics,Bioinformatics","https://github.com/bonsai-team/Porechop_ABI","Porechop_ABI (ab initio) is an extension of Porechop whose purpose is to process adapter sequences in ONT reads.","conda","false","false"
"preseq","2.0.3-conda","prediction-and-recognition","Genomics,DNA,Sequencing","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"
"pretextmap","0.1.9-conda","data-handling","Epigenetics,Sequence assembly","https://github.com/wtsi-hpag/PretextMap","Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.","conda","true","false"
"pretextsnapshot","0.0.4-conda","visualisation","Epigenetics,Sequence assembly","https://github.com/wtsi-hpag/PretextSnapshot","Commandline image generator for Pretext contact maps","conda","true","false"
"Prinseq","0.20.4-conda","read-pre-processing","Genomics,Transcriptomics,Metagenomics","http://edwards.sdsu.edu/prinseq","PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.","conda","false","false"
"ProbCons","1.12-shell","sequence-comparison","Sequence analysis","http://probcons.stanford.edu/","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","Model organisms,Genomics,Virology","https://github.com/tseemann/prokka","Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.","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","genetic-variation-analysis","Sequence assembly","https://github.com/SexGenomicsToolkit/PSASS","Software to compare pooled sequencing datasets from two groups (usually two sexes).","conda","false","false"
"purge_dups","1.2.6-conda","genome-assembly","Sequence assembly","https://github.com/dfguan/purge_dups","Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences","conda","true","false"
"pycoQC","2.5.2-conda,2.5.0.19-conda","sequencing-quality-control","Sequence analysis,Data quality management,Sequencing","https://a-slide.github.io/pycoQC/","PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.","conda","true","false"
"pyScaf","0.12a-conda","scaffolding","Sequence assembly","https://github.com/lpryszcz/pyScaf","Orders contigs from genome assemblies","conda","false","false"
"pysradb","1.4.2-conda","deposition","Gene transcripts,Bioinformatics,Sequencing","https://github.com/saketkc/pysradb","Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.","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","2022.2-conda,2022.11-conda,2019.10-conda","analysis","Biology","http://qiime.org/","Open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. The pipeline is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations.","conda","false","false"
"qualimap","2.2.2d-conda","sequencing-quality-control","Data quality management","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","prediction-and-recognition","Virology,Sequencing,Machine learning,Genetics,RNA","https://github.com/cbg-ethz/QuasiRecomb","Software of Inference of Quasispecies subjected to Recombination. We present a jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. We offer an implementation of the EM algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies.","conda","false","false"
"QUAST","5.0.2-conda,5.0.0-conda,4.6.3-conda,4.5-conda","visualisation","Sequence assembly","http://quast.sourceforge.net/quast","QUAST stands for QUality ASsessment Tool.  ","conda","false","false"
"r-gplots","3.1.1-conda","data-visualisation","Data visualisation","https://CRAN.R-project.org/package=gplots","Various R programming tools for plotting data","conda","true","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","4.2.1-conda,4.1.1-conda,4.0.0-conda,3.6.1-conda,3.5.1-conda","analysis","Data architecture, analysis and design,Mathematics,Statistics and probability","http://www.r-project.org/","Free software environment for statistical computing and graphics.","conda","false","false"
"ra","0.2.1-shell","genome-assembly","Genomics,Sequence assembly","https://github.com/lbcb-sci/ra","Assembler for raw de novo genome assembly of long uncorrected reads.","shell","false","false"
"Racon","1.4.20-conda,1.4.10-conda","genome-assembly","Whole genome sequencing,Sequence assembly,Plant biology","https://github.com/isovic/racon","The Possibility to Use Oxford Nanopore Technology | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here: | Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step | Consensus module for raw de novo DNA assembly of long uncorrected reads","conda","false","false"
"ragout","2.3-conda","genome-assembly","Sequence analysis,Sequence assembly,DNA","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","RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.","conda","false","false"
"RAiSD","2.9-shell","genetic-variation-analysis","Population genetics","https://github.com/alachins/raisd","Software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors","shell","false","false"
"Raven","1.5-conda,0.0.7-conda","de-novo-assembly","Genomics,Whole genome sequencing,Sequence assembly","https://github.com/lbcb-sci/raven","a de novo genome assembler for long reads.","conda","false","false"
"RAxML","8.2.12-conda","sequence-analysis","Phylogenetics,Sequence analysis","http://sco.h-its.org/exelixis/web/software/raxml/","A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.","conda","false","false"
"Rcorrector","1.0.4-conda,1.0.3-conda","sequencing-error-detection","Sequencing,RNA,RNA-Seq","https://github.com/mourisl/Rcorrector/","This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.","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"
"recentrifuge","1.10.0-conda","taxonomic-classification","Microbial ecology,Metagenomic sequencing,Metagenomics","https://sites.google.com/view/recentrifuge","Robust comparative analysis and contamination removal for metagenomics.","conda","false","false"
"regtools","1.0.0-conda","data-handling","Transcriptomics","https://regtools.readthedocs.io/en/latest/","Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.","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","k-mer-counting","Sequence composition, complexity and repeats,Sequence assembly,Sequencing","https://github.com/Reedwarbler/REPdenovo","A new method which assembles repeat sequences directly from raw shotgun sequencing data.","conda","false","false"
"repeatmasker","4.1.2-p1-conda","genome-annotation","Sequence composition, complexity and repeats,Sequence analysis","http://www.repeatmasker.org/","A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).","conda","true","false"
"RepeatModeler","2.0.1-conda,1.0.11-conda","repeat-sequence-detection","Sequence composition, complexity and repeats","http://www.repeatmasker.org/RepeatModeler/","De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.","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"
"ribodetector","0.2.7-conda","sequence-comparison","Genomics","https://github.com/hzi-bifo/RiboDetector","RiboDetector is a software developed to accurately yet rapidly detect and remove rRNA sequences from metagenomeic, metatranscriptomic, and ncRNA sequencing data. It was developed based on LSTMs and optimized for both GPU and CPU.","conda","false","false"
"roary","3.13.0-conda","genome-assembly","Mapping,Genomics,DNA","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"
"rseqc","2.6.4-conda","data-handling","Sequencing","http://rseqc.sourceforge.net","Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.","conda","true","false"
"RStudio","1.1.456-conda","data-handling","Data architecture, analysis and design,Mathematics,Statistics and probability","https://www.rstudio.com/","Integrated development environment (IDE) for the R programming language.","conda","false","false"
"salmon","1.6-conda,1.5.2-conda,1.3.0-conda,1.10.0-conda,0.14.1-conda,0.13.1-conda","sequence-composition-calculation","Transcriptomics,Gene expression,RNA-Seq","https://combine-lab.github.io/salmon","A tool for transcript expression quantification from 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","true","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","4.0.0-Nextflow,3.0.1-Nextflow,2.0.0-Nextflow","scaffolding","Mapping,Sequence assembly,Sequencing","https://github.com/alekseyzimin/masurca","The SAMBA tool uses long reads to improve the contiguity of genome assemblies.","Nextflow","false","false"
"sambamba","0.8.0-conda,0.6.6-conda","sequence-analysis","Sequence analysis,DNA,RNA-Seq","http://www.open-bio.org/wiki/Sambamba","This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats.","conda","false","false"
"samblaster","0.1.26-conda","split-read-mapping","Mapping,DNA,Sequencing","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,1.16.1-conda,1.14-conda,1.13-conda,1.11-conda,1.10-conda","indexing","Rare diseases,Mapping,Sequence analysis,Sequencing","http://www.htslib.org/","SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.","conda","false","false"
"Sarek","3.0.1-shell","sample-comparison","Genomics,Workflows,Whole genome sequencing,Oncology","https://nf-co.re/sarek","Sarek is part of nf-core and has changed to the nf-core-sarek id.","shell","false","false"
"sartools","1.7.3-conda,1.6.3-conda,1.3.2-conda","standardisation-and-normalisation","Transcriptomics,Statistics and probability","https://github.com/PF2-pasteur-fr/SARTools","R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis.","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"
"SENSV","1.0.4-conda","variant-calling","Comparative genomics","https://github.com/HKU-BAL/SENSV","A tool to detect structural variant","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","2.4.0-conda,2.3.1-conda,2.2.0-conda,2.1.0-conda,2.0.0-conda,0.9.1-conda","dna-transcription","Sequence analysis,Database management","https://bioinf.shenwei.me/seqkit/","FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.","conda","false","false"
"SeqTk","1.3-conda,1.2-conda","data-handling","Data management","https://github.com/lh3/seqtk","A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.","conda","true","false"
"SGA","0.10.15-conda","sequence-assembly","Genomics,Sequence assembly,Whole genome sequencing","https://github.com/jts/sga","SGA is a de novo assembler designed to assemble large genomes from high coverage short read data.","conda","false","false"
"sgtr","1.1.4-conda","genetic-mapping","DNA polymorphism","https://github.com/SexGenomicsToolkit/sgtr","R package to visualize results from population genomics analyses. The package implements low-level function to generate genomics plots and high-level functions to visualize results from the Sex Genomics Toolkit.","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","Genomics,Sequence assembly","https://github.com/chanzuckerberg/shasta","De novo assembly from Oxford Nanopore reads.","shell","false","false"
"ShoRAH","1.1.0-conda","haplotype-mapping","Genetics,Metagenomics,Sequencing","https://github.com/cbg-ethz/shorah","Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.","conda","false","false"
"shovill","1.1.0-conda,1.0.9-conda","genome-assembly","Genomics,Sequence assembly,Microbiology","https://github.com/tseemann/shovill","Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.","conda","true","false"
"signalP","6.0g-singularity,5.0b-shell,4.1-shell","protein-signal-peptide-detection","Protein sites, features and motifs","http://cbs.dtu.dk/services/SignalP/","Prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms.","singularity,shell","false","false"
"Simka","1.4-shell","sequence-distance-matrix-generation","Metagenomics","https://github.com/GATB/simka","Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.","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,Workflows,Software engineering","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","2.0.6-conda,1.0.7-conda,1.0.12-conda","sequence-analysis","Sequencing,DNA structural variation","https://github.com/fritzsedlazeck/Sniffles","An algorithm for structural variation detection from third generation sequencing alignment.","conda","false","false"
"Snippy","4.6.0-conda,4.1.0-conda","phylogenetic-tree-visualisation","Model organisms,Genomics,Phylogenetics,DNA polymorphism","https://github.com/tseemann/snippy","Rapid haploid variant calling and core SNP phylogeny generation.","conda","false","false"
"SNP-sites","2.5.1-conda","variant-calling","Comparative genomics","https://github.com/sanger-pathogens/snp-sites","Rapidly extracts SNPs from a multi-FASTA alignment.","conda","false","false"
"snpeff","5.0-conda,4.5covid19-conda,4.3.1t-conda,4.3-conda","snp-detection","DNA polymorphism,Genetic variation,Nucleic acid sites, features and motifs","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","Data architecture, analysis and design,Data management","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","sequence-assembly","Sequence assembly","http://soap.genomics.org.cn/soapdenovo.html","SOAPdenovo, a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds.","conda","false","false"
"SortMeRNA","4.2.0-conda,2.1b-conda","sequence-similarity-search","Transcriptomics","http://bioinfo.lifl.fr/RNA/sortmerna/","Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.","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-search","Computational biology","https://sourmash.readthedocs.io/en/latest/","Compute and compare MinHash signatures for DNA data sets.","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","genome-assembly","Sequence assembly","http://cab.spbu.ru/software/spades/","St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.","conda","false","false"
"squeezemeta","1.6.1-conda","read-binning","RNA-Seq,Metatranscriptomics,Metagenomics,Microbial ecology","https://github.com/jtamames/SqueezeMeta","SqueezeMeta is a fully automated metagenomics pipeline, from reads to bins.","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","2.64-bash,2.59-shell,2.55-conda,2.52-conda,2.0Beta9-conda,2.0Beta8-conda,1.46-conda","data-handling","Population genetics,Mapping","http://catchenlab.life.illinois.edu/stacks/","Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.","bash,shell,conda","false","false"
"star","2.7.9a-conda,2.7.8a-conda,2.7.2c-conda,2.7.10b-conda,2.7.10a-conda,2.7.0d-conda,2.5.3a-conda","sequence-alignment","Transcriptomics,RNA-Seq","http://code.google.com/p/rna-star/","Ultrafast universal RNA-seq data 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","2.2.0-conda,2.1.4-conda","transcriptome-assembly","Transcriptomics,RNA-seq","https://ccb.jhu.edu/software/stringtie/","Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.","conda","false","false"
"Structure","2.3.4-conda","genetic-variation-analysis","Population genetics","http://web.stanford.edu/group/pritchardlab/structure.html","The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.","conda","false","false"
"Subread","2.0.1-conda","read-mapping","Mapping,Whole genome sequencing,RNA-Seq,Sequencing","http://subread.sourceforge.net/","Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called "seed-and-vote" to achieve fast, accurate and scalable read mapping. It automatically determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports indel detection and can map reads with both fixed and variable lengths.","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","3.1.3-conda,3.1.0-conda","sequence-clustering","Sequence analysis,Biodiversity,Microbiology,Molecular biology","https://github.com/torognes/swarm","A robust and fast clustering method for amplicon-based studies. The purpose of this tool is to provide a novel clustering algorithm that handles massive sets of amplicons.","conda","false","false"
"SyRi","1.5.4-conda","haplotype-mapping","DNA polymorphism,Mapping,Sequence assembly,Sequencing,DNA structural variation","https://schneebergerlab.github.io/syri/","SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies.","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","Genomics","http://www.htslib.org/doc/tabix.html","Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file (in.tab.bgz.tbi or in.tab.bgz.csi) when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface.","conda","false","false"
"TaxMapper","1.0.2-conda","genetic-mapping","Mapping,NGS,Microbiology,Taxonomy","https://bitbucket.org/dbeisser/taxmapper","Analysis tool for a reliable mapping to a provided microeukaryotic reference database and part of a comprehensive Snakemake workflow. It is used to assign taxonomic information to each NGS read by mapping to the database and filtering low quality assignments.","conda","false","false"
"taxonkit","0.8.0-conda,0.14.1-conda","formatting","Biotechnology,Ecology,Taxonomy","https://github.com/shenwei356/taxonkit","TaxonKit is 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"
"tigmint","1.2.6-conda","scaffolding","Structural variation,Sequence assembly","https://github.com/bcgsc/tigmint","Tigmint is a tool for correcting misassemblies in genome assembly drafts using linked or long sequencing reads","conda","false","false"
"TMHMM","2.0-shell","transmembrane-protein-prediction","Protein modifications,Proteomics,Protein secondary structure,Membrane and lipoproteins,Protein folds and structural domains","http://cbs.dtu.dk/services/TMHMM/","Prediction of transmembrane helices in proteins.","shell","true","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","RNA-seq","http://ccb.jhu.edu/software/tophat/index.shtml","Gapped-read mapper for RNA-seq data.","conda","true","false"
"Tractor","master-conda","genotyping","Workflows,GWAS study,Genotype and phenotype,Lipids","https://github.com/eatkinson/Tractor","A framework allowing for improved inclusion of admixed individuals in large-scale association studies.","conda","false","false"
"Trans-ABySS","2.0.1-conda","de-novo-assembly","Transcriptomics,Sequence assembly,Gene structure,RNA-Seq","http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss","A pipeline for de novo short-read transcriptome assembly and analyses.","conda","false","false"
"TransDecoder","5.5.0-conda,3.0.1-conda","coding-region-prediction","Gene transcripts,Genomics","https://github.com/TransDecoder/TransDecoder/wiki","TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.","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","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. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. The allele frequencies in the modern populations are used to infer the structure of this graph.","conda","false","false"
"trf","4.09.1-conda","repeat-sequence-detection","Sequence composition, complexity and repeats,Sequence analysis","http://tandem.bu.edu/trf/trf.html","Tandem Repeats Finder. Find tandem repeats in DNA sequences without the need to specify either the pattern or pattern size. It uses the method of k-tuple matching to avoid the need for full scale alignment matrix computations. It requires no a priori knowledge of the pattern, pattern size or number of copies. There are no restrictions on the size of the repeats that can be detected. It determines a consensus pattern for the smallest repetitive unit in the tandem repeat.","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","multiple-sequence-alignment","Sequence analysis,Sequence sites, features and motifs,Sequencing","http://trimal.cgenomics.org","Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.","conda","true","false"
"Trimmomatic","0.36-conda","sequence-trimming","Sequence analysis,Data quality management,Sequencing","http://www.usadellab.org/cms/index.php?page=trimmomatic","A flexible read trimming tool for Illumina NGS data","conda","true","false"
"Trinity","2.8.5-conda,2.8.4-conda,2.5.1-conda,2.4.0-conda","transcriptome-assembly","Gene transcripts,Transcriptomics,Gene expression","https://github.com/trinityrnaseq/trinityrnaseq/wiki","Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.","conda","false","false"
"Trinotate","3.1.1-conda","gene-functional-annotation","Transcriptomics,Gene expression","https://github.com/Trinotate/Trinotate.github.io","Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.","conda","true","false"
"trnascan-se","2.0.7-conda","trna-gene-prediction","Genomics,Sequence analysis,RNA","http://trna.ucsc.edu/tRNAscan-SE/","A program for improved detection of transfer RNA genes in genomic sequence.","conda","false","false"
"Trycycler","0.5.3-conda,0.5.0-conda","genome-assembly","Sequence assembly,Human biology,DNA,Whole genome sequencing,Genomics","http://github.com/rrwick/Trycycler-paper","Trycycler: consensus long-read assemblies for bacterial genomes","conda","false","false"
"TSEBRA","1.0.3-conda","homology-based-gene-prediction","Model organisms,Gene transcripts,Gene expression,RNA-Seq","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","Genomics,DNA","https://genome.ucsc.edu/goldenPath/help/twoBit.html","Convert DNA from fasta to 2bit format","conda","false","false"
"UGENE","1.32.0-shell","visualisation","Sequence analysis,Phylogenetics,Genomics,Protein structure analysis","http://ugene.unipro.ru","UGENE is a free cross-platform genome analysis suite that combines popular bioinformatics tools within a single user friendly interface.","shell","false","false"
"Unicycler","0.5.0-conda,0.4.8-conda","genome-assembly","Genomics,Sequence assembly,Microbiology,Sequencing","https://github.com/rrwick/Unicycler","A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.","conda","true","false"
"vadr","1.1-singularity","deposition","Virology,Small molecules,Genomics,Sequence sites, features and motifs,Gene and protein families","https://github.com/nawrockie/vadr","Classification and annotation of viral sequences based on RefSeq annotation.","singularity","false","false"
"validatefastq","0.1.1-conda","format-validation","Genomics,Data quality management","https://biopet.github.io/validatefastq/0.1.1/index.html","This tool validates a FASTQ file. When data is paired it can also validate a pair of FASTQ files. ValidateFastq will check if the FASTQ is in valid FASTQ format. This includes checking for duplicate reads and checking whether a pair of FASTQ files contains the same amount of reads and headers match. It also check whether the quality encodings are correct and outputs the most likely encoding format (Sanger, Solexa etc.).","conda","false","false"
"vamb","3.0.3-gpu-conda,3.0.3-conda","scaffolding","Sequence assembly,Microbial ecology,Machine learning,Informatics,Metagenomics","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","DNA polymorphism,Sequencing","http://dkoboldt.github.io/varscan/","VarScan, an open source tool for variant detection that is compatible with several short read align-ers.","conda","true","false"
"vcflib","1.0.0_rc1-conda","data-handling","Genomics,Data management","https://github.com/vcflib/vcflib","API and command line utilities for the manipulation of VCF files.","conda","false","false"
"VCFTools","0.1.16-conda,0.1.14-conda","data-handling","Genetic variation","https://vcftools.github.io/index.html","Provide easily accessible methods for working with complex genetic variation data in the form of VCF files.","conda","false","false"
"Velvet","1.2.10-conda","formatting,de-novo-assembly","Sequence assembly","https://github.com/dzerbino/velvet","A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.","conda","true","false"
"VGAS","0.0.2020.07.22-conda","genome-annotation","Genomics","http://cefg.uestc.cn/vgas","VGAS is a system combing ab initio method and similarity-based method, which can perform the functions of virus gene finding and function annotating merely depending on the gene sequence itself","conda","false","false"
"viennarna","2.5.1-conda","rna-secondary-structure-prediction","Nucleic acid structure analysis,RNA,Structure prediction","https://www.tbi.univie.ac.at/RNA/","The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.","conda","false","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","dna-mapping","Sequence analysis,Metagenomics","https://github.com/torognes/vsearch","High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.","shell","false","false"
"vt","2015.11.10-conda","variant-calling","Genetics,Sequence analysis,Sequence sites, features and motifs,Sequencing","http://genome.sph.umich.edu/wiki/Vt","Variant tool set that discovers short variants from Next Generation Sequencing data.","conda","false","false"
"vulcan","1.0.3-conda","enrichment-analysis","Systems biology,ChIP-seq,Gene expression","http://bioconductor.org/packages/release/bioc/html/vulcan.html","VirtUaL ChIP-Seq Analysis through Networks is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data.","conda","false","false"
"w2rap-contigger","2019-07-11-shell","genome-assembly","Genomics,Sequence assembly","https://github.com/bioinfologics/w2rap-contigger","An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.","shell","false","false"
"wengan","0.1-shell","genome-assembly","Human biology,Whole genome sequencing,Sequence assembly","https://github.com/adigenova/wengan","Wengan is a new genome assembler that unlike most of the current long-reads assemblers avoids entirely the all-vs-all read comparison.","shell","false","false"
"WhatsHap","1.0-conda,0.18-conda","genotyping","DNA polymorphism,Sequence assembly","http://whatshap.readthedocs.io","Software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads.","conda","false","false"
"WHdenovo","14012020-conda","phasing","Model organisms,Sequence assembly,Sequencing","https://github.com/shilpagarg/WHdenovo","A haplotype-aware de novo assembly of related individuals using pedigree sequence graph.","conda","false","false"
"winnowmap","2.03-conda","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. Winnowmap development began on top of minimap2 codebase, and since then we have incorporated the following two ideas to improve mapping accuracy within repeats","conda","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","sequence-assembly","Machine learning,Mapping,Sequence assembly","https://github.com/natir/yacrd","upstream tools for long-read genome assembly.","conda","false","false"
"yahs","1.2a-shell,1.1a.2-shell","scaffolding","DNA binding sites,Sequence assembly","https://github.com/c-zhou/yahs","YaHS is scaffolding tool using Hi-C data. It relies on a new algorithm for contig joining detection which considers the topological distribution of Hi-C signals aiming to distinguish real interaction signals from mapping noises.","shell","false","false"
"yak","0.1-shell","k-mer-counting","Sequence assembly","https://github.com/lh3/yak","Yet another k-mer analyzer ","shell","false","false"
"zUMIs","2.7.0-conda","mapping","Mapping,Sequence analysis,RNA-Seq","https://github.com/sdparekh/zUMIs","A fast and flexible pipeline to process RNA sequencing data with UMIs.","conda","false","false"