jbrowse : A modern genome browser built with JavaScript and HTML5.
author: GMOD
created: 2009-01-16 11:30:52
bioinformatics biology genome-annotation genome-browser genomics protein-annotation javascript


Artemis : Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
author: sanger-pathogens
created: 2009-09-30 12:46:38
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing java


goatools : Python scripts to find enrichment of GO terms
author: tanghaibao
created: 2010-01-15 19:15:21
fdr gene-ontology gene-set-enrichment genomics python


sequenceserver : Intuitive local web frontend for the BLAST bioinformatics tool
author: wurmlab
created: 2010-10-01 06:19:41
bioinformatics blast genomics genomics-visualization sequence-alignment sequencing visualization javascript


jcvi : Python utility libraries on genome assembly, annotation and comparative genomics
author: tanghaibao
created: 2010-12-01 23:18:02
comparative-genomics genetic-algorithm genetic-maps genome-sequencing genomics sequence-alignments variant-calling python


bwa : Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
author: lh3
created: 2011-01-14 01:36:33
bioinformatics fm-index genomics sequence-alignment c


gubbins : Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
author: sanger-pathogens
created: 2011-11-01 12:41:33
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing c


fermi : A WGS de novo assembler based on the FMD-index for large genomes
author: lh3
created: 2012-01-06 20:21:54
bioinformatics denovo-assembly genomics c


snp-sites : Finds SNP sites from a multi-FASTA alignment file
author: sanger-pathogens
created: 2012-01-24 09:32:47
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing c


intermine : A powerful open source data warehouse system
author: intermine
created: 2012-07-02 10:25:18
api bioinformatics biology clojure clojurescript data-visualisation data-visualization data-warehouse genetics genomics java lgplv3 open-source opensource perl postgresql python tomcat tomcat8 webservices


mapping-iterative-assembler : Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria
author: mpieva
created: 2012-07-02 14:34:39
alignment bioinformatics consensus-calling contamination genomics mitochondria c


mlst_check : Multilocus sequence typing by blast using the schemes from PubMLST
author: sanger-pathogens
created: 2012-07-23 15:23:36
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing perl


assembly_improvement : Improve the quality of a denovo assembly by scaffolding and gap filling
author: sanger-pathogens
created: 2012-08-15 15:57:48
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing perl


FALDO : Feature Annotation Location Description Ontology
author: OBF
created: 2012-09-07 02:20:53
biology genomics ontology proteomics uniprot xslt


bowtie2 : A fast and sensitive gapped read aligner
author: BenLangmead
created: 2012-12-20 19:25:11
bioinformatics c-plus-plus genomics read-aligners c++


ngless : NGLess: NGS with less work
author: ngless-toolkit
created: 2013-01-08 15:56:55
bioinformatics bioinformatics-pipeline bwa fastq fastq-format genomics haskell haskell-language metagenomics next-generation-sequencing ngs samtools science


stacks_workflow : RADseq workflow built around STACKS
author: enormandeau
created: 2013-03-26 13:18:34
gbs genomics stacks python


qqman : An R package for creating Q-Q and manhattan plots from GWAS results
author: stephenturner
created: 2013-04-02 10:45:40
cran genomics gwas r


biojava : :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
author: biojava
created: 2013-04-03 16:27:17
bioinformatics genomics java parser-library pdb protein-data-bank protein-modification protein-sequences protein-structure sequence-alignment structural-bioinformatics structure-alignment


arvados : An open source platform for managing and analyzing biomedical big data
author: curoverse
created: 2013-04-11 01:06:19
arvados aws azure bigdata bioinformatics cloud cluster cwl docker gcp genomics go python ruby workflow


Roary : Rapid large-scale prokaryote pan genome analysis
author: sanger-pathogens
created: 2013-04-18 13:53:50
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing perl


Bio-Tradis : A set of tools to analyse the output from TraDIS analyses
author: sanger-pathogens
created: 2013-05-22 13:42:45
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing perl


genometools : GenomeTools genome analysis system.
author: genometools
created: 2013-07-04 13:39:38
annotation bioinformatics c genome genometools genomics gff3 library lua python repeats ruby toolkit


chanjo : Chanjo provides a better way to analyze coverage data in clinical sequencing.
author: Clinical-Genomics
created: 2013-07-05 13:22:17
bioconda coverage genomics python sambamba sql


deepTools : Tools to process and analyze deep sequencing data.
author: deeptools
created: 2013-07-08 12:30:28
bioinformatics chip-seq genomics ngs python rna-seq


GEOquery : The bridge between the NCBI Gene Expression Omnibus and Bioconductor
author: seandavi
created: 2013-07-19 06:44:10
bioconductor bioinformatics data-science genomics ncbi-geo r rstats


MultiAssayExperiment : Bioconductor package for management of multi-assay data
author: waldronlab
created: 2013-07-22 03:29:27
bioconductor bioconductor-package genomics nci-itcr r tcga


wgs2ncbi : Toolkit for preparing genomes for submission to NCBI
author: naturalis
created: 2013-08-06 13:15:44
bioinformatics dataset genome-annotation genomics perl


Fastaq : Python3 scripts to manipulate FASTA and FASTQ files
author: sanger-pathogens
created: 2013-09-06 11:54:45
bioinformatics genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing python


bedops : :microscope: BEDOPS: high-performance genomic feature operations
author: bedops
created: 2013-09-18 19:43:30
bed bedops bioinformatics c c-plus-plus compression conversion genomics parallel pipeline set set-theory toolkit


biojava-tutorial : :book::books:An introductory tutorial for BioJava
author: biojava
created: 2013-09-18 20:23:45
3d-structure bioinformatics biojava genomics java protein-disorder protein-structure tutorial python


vcfR : Tools to work with variant call format files
author: knausb
created: 2013-10-28 17:09:04
genomics population-genetics population-genomics rcpp rstats vcf-data visualization r


intermine-ws-python : InterMine Client library in Python
author: intermine
created: 2013-11-14 15:23:12
bioinformatics genomics python


dna-traits : A fast 23andMe genome text file parser, now superseded by arv
author: cslarsen
created: 2014-01-05 22:45:02
23andme bioinformatics dna genomics health-report python snpedia snps


cljam : A DNA Sequence Alignment/Map (SAM) library for Clojure
author: chrovis
created: 2014-01-08 09:52:14
2bit bam bcf bed bigwig bioinformatics clojure fasta fastq genomics gff sam vcf wig


bac-genomics-scripts : Collection of scripts for bacterial genomics
author: aleimba
created: 2014-01-09 08:24:59
annotation bioinformatics bioperl blast computational-biology genomics microbial-genomics microbiology mlst ngs opensource perl science scripts-collection sequencing unix


Bio.jl : Bioinformatics and Computational Biology Infrastructure for Julia
author: BioJulia
created: 2014-01-23 22:20:21
bioinformatics biology dna genomics julia


EDGE : EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.
author: LANL-Bioinformatics
created: 2014-01-28 17:50:53
bioinformatics genomics perl


assembly-stats : Get assembly statistics from FASTA and FASTQ files
author: sanger-pathogens
created: 2014-04-04 10:43:34
bioinformatics genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing c++


smof : Explore and analyze biological sequence data
author: incertae-sedis
created: 2014-04-27 12:34:29
bioinformatics biology fasta genomics sequence sequence-analysis python


htsjdk : A Java API for high-throughput sequencing data (HTS) formats.
author: samtools
created: 2014-04-29 10:11:28
bam cram dna fasta genomics ngs sam sequencing java


iva : de novo virus assembler of Illumina paired reads
author: sanger-pathogens
created: 2014-04-30 09:44:21
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing python


mccortex : De novo genome assembly and multisample variant calling
author: mcveanlab
created: 2014-05-07 23:23:02
contigs cortex de-bruijn-graphs genome-analysis genome-assembly genome-graph genomics kmer variant-calling c


sample : Performs memory-efficient reservoir sampling on very large input files delimited by newlines
author: alexpreynolds
created: 2014-05-29 22:15:33
bed bioinformatics c genomics reservoir-sampling sampling


aroma.seq : 🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework
author: HenrikBengtsson
created: 2014-06-15 04:46:25
bioinformatics distributed-computing framework genomics hpc ht-seq large-scale package parallel r


defining_genomic_regions : Define regions in the genome
author: davetang
created: 2014-06-18 10:29:22
bedtools genomics perl


Teaching-EMBL-Plant-Path-Genomics : Presentation and example material for the EMBL Plant and Pathogen Genomics workshop, 8-11 July 2014
author: widdowquinn
created: 2014-07-08 06:38:10
bioinformatics genomics plant-pathogens teaching teaching-materials jupyter notebook


orthologr : Comparative Genomics with R
author: HajkD
created: 2014-07-08 08:01:29
blast blast-searches codon-alignment comparative comparative-genomics-studies dnds-estimation genomics orthology-inference r sequence-alignments


bio : General bioinformatics functions in Python
author: mattravenhall
created: 2014-07-25 11:47:21
bioinformatics bioinformatics-algorithms genomics python


biomartr : Genomic Data Retrieval with R
author: ropensci
created: 2014-08-05 15:34:55
biomart database-retrieval ensembl-servers genome genome-annotation genome-retrieval genomics meta-analysis metagenomics ncbi-genbank peer-reviewed proteome r r-package rstats sequenced-genomes


svtyper : Bayesian genotyper for structural variants
author: hall-lab
created: 2014-08-14 18:06:49
bioinformatics genomics genotype vcf python


genome-explorer : :microscope: Social network for Bacteria
author: audy
created: 2014-09-05 20:41:16
bioinformatics genomics rails-application ruby


SCUBAT2 : Scaffolding contigs with transcripts
author: GDKO
created: 2014-09-20 23:21:39
bioinformatics genomics scaffolding python


viral-ngs : Viral genomics analysis pipelines
author: broadinstitute
created: 2014-09-25 19:00:24
bam fastq genome genome-assembly genome-sequencing genomics illumina variant-annotations variant-calling viral viral-ngs python


gff3toembl : Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
author: sanger-pathogens
created: 2014-10-01 10:28:25
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing python


vg : tools for working with genome variation graphs
author: vgteam
created: 2014-10-02 16:54:27
dna genome-graph genomics graph variation-graph c++


igvfox : firefox addon : IGV (Integrative Genomics Viewer) control through mozilla Firefox
author: lindenb
created: 2014-10-16 10:30:21
addon bam bioinformatics firefox genomics igv javascript mozilla-firefox plugin socket visualization xpi


Exomiser : A Tool to Annotate and Prioritize Exome Variants
author: exomiser
created: 2014-11-04 10:09:50
analysis exome genomics monarchinitiative phenotypes variants java


pathogens-vm : To build a virtual machine with some Sanger pathogens software installed
author: sanger-pathogens
created: 2014-11-10 09:17:52
bioinformatics genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing shell


MetamapsDB : Structured Queries and analyses used with MetamapsDB
author: etheleon
created: 2014-11-14 07:43:36
bioinformatics genomics metagenomics microbial-communities r


wiggleplotr : A small R package to make sequencing read coverage plots in R.
author: kauralasoo
created: 2014-11-18 22:52:41
atac-seq genomics rna-seq r


sequencework : programs and scripts, mainly python, for analyses related to nucleic or protein sequences
author: fomightez
created: 2014-11-24 17:57:05
bioinformatics bioinformatics-analysis bioinformatics-scripts dna genomics list lists protein-sequences python rna


pyplink : Python module to read binary Plink files.
author: lemieuxl
created: 2014-12-02 14:34:17
bioinformatics genetics genomics python


gatk : Official code repository for GATK versions 4 and up
author: broadinstitute
created: 2014-12-02 20:50:36
bioinformatics dna gatk genome genomics ngs science sequencing spark java


pyGenClean : Automated genetic data clean up procedure in Python.
author: lemieuxl
created: 2014-12-02 21:09:22
bioinformatics genetics genomics python


reads2genome : From second generation sequencing reads to annotated bacterial genome
author: mgalardini
created: 2014-12-08 15:35:32
bioinformatics genome-assembly genomics microbiology pipeline reproducible-science python


smallrnaseq : small rna-seq analysis package
author: dmnfarrell
created: 2014-12-15 22:58:05
bioinformatics genomics mirna python rna-seq sequencing smallrna


gatb-core : Core library of the Genome Analysis Toolbox with de-Bruijn graph
author: GATB
created: 2014-12-25 15:35:42
bioinformatics de-bruijn-graphs gatb genomics c++


bfc : High-performance error correction for Illumina resequencing data
author: lh3
created: 2014-12-30 21:34:14
bioinformatics genomics tex


bioio : Lightweight C++ library for reading FASTA and FASTQ files.
author: dancooke
created: 2015-01-05 14:32:22
fasta fastq genomics c++


catch : A package for designing compact and comprehensive probe sets.
author: broadinstitute
created: 2015-01-05 16:36:28
bioinformatics dna genome genomics ngs science sequencing viral python


mvftools : Multisample Variant Format ToolKit
author: jbpease
created: 2015-02-01 17:53:19
genomics molecular-evolution phylogenetics phylogenomics population-genetics population-genomics python


ideogram : Chromosome visualization with D3.js
author: eweitz
created: 2015-02-04 03:05:48
cancer-genomics comparative-genomics cytogenetics genomics karyotype personal-genomics visualization javascript


octopus : Bayesian haplotype-based mutation calling
author: luntergroup
created: 2015-02-04 09:24:53
bioinformatics de-novo-mutation genomics haplotypes phasing somatic-variants variant-calling variants c++


companion : Pipeline for automatic eukaryotic parasite annotation
author: sanger-pathogens
created: 2015-02-05 15:23:06
annotation bioinformatics genome genomics lua nextflow parasites pipeline


genipe : Genome-wide imputation pipeline
author: pgxcentre
created: 2015-02-09 18:44:51
bioinformatics genetics genomics python


VitisOmics : Open and reproducible handling of "omics" data for the Vitis genus.
author: timflutre
created: 2015-02-09 22:28:46
genomics grapevine reproducible-research r


ariba : Antimicrobial Resistance Identification By Assembly
author: sanger-pathogens
created: 2015-02-11 10:13:06
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing python


seqstats : Biological Sequence Statistics in R
author: HajkD
created: 2015-02-12 09:52:35
bioinformatics biological-data-analysis biological-sequence-statistics biological-sequences genomics r


TARGet : Topological inference of horizontal evolution from multiple sequence alignments
author: CamaraLab
created: 2015-02-25 20:06:21
genomics recombination topological-data-analysis c++


BGData : A Suite of Packages for Analysis of Big Genomic Data
author: QuantGen
created: 2015-03-16 21:33:22
genetics genomics gwas r r-pkg


fermikit : De novo assembly based variant calling pipeline for Illumina short reads
author: lh3
created: 2015-04-11 04:04:05
bioinformatics denovo-assembly genomics variant-calling tex


stategraems : STATegra EMS: an Experiment Management System for complex next-generation omics experiments
author: fikipollo
created: 2015-04-15 06:17:17
annotation bioinformatics ems genomics metabolomics metadata ngs omics-experiments proteomics reproducibility reproducible-science rna-seq java


circlator : A tool to circularize genome assemblies
author: sanger-pathogens
created: 2015-04-16 09:34:48
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing python


hap.py : Haplotype VCF comparison tools
author: Illumina
created: 2015-04-28 12:43:18
bioinformatics genomics vcf vcf-comparison c++


vcfanno : annotate a VCF with other VCFs/BEDs/tabixed files
author: brentp
created: 2015-04-29 16:00:43
annotation bioinformatics genomics vcf go


bgt : Flexible genotype query among 30,000+ samples whole-genome
author: lh3
created: 2015-05-02 04:38:40
bioinformatics genomics c


StratiPy : Graph regularized nonnegative matrix factorization (GNMF) in Python
author: GHFC
created: 2015-05-06 13:30:59
bioinformatics genomics graph nmf ppi python stratification jupyter notebook


reads2snps : From second generation sequencing reads to variant calls
author: mgalardini
created: 2015-05-08 11:10:46
bioinformatics call-variants genomics pipeline reproducible-science variant-calls makefile


Pathifier-Tool-Kit : Scripts that may help you use PATHIFIER (Drier et al., 2013)
author: AngelCampos
created: 2015-05-11 03:05:01
bioinformatics genomics r


PGA : PGA: a tool for ProteoGenomics Analysis
author: wenbostar
created: 2015-05-11 03:23:56
genomics proteogenomics proteomics transcriptomics r


ntHash : ntHash: recursive nucleotide hashing
author: bcgsc
created: 2015-05-15 18:44:10
bioinformatics bloom-filter genomics hash hash-algorithm hash-methods k-mer-hashing c++


pangenome_variation : Run several analysis on bacterial genomes
author: mgalardini
created: 2015-05-18 10:53:44
bioinformatics genomics microbiology python


simplesam : Simple pure Python SAM parser and objects for working with SAM records
author: mdshw5
created: 2015-05-20 01:15:54
bam bioinformatics genomics python sam


tag : Genome annotation data analysis and management implemented in pure Python
author: standage
created: 2015-05-21 18:04:45
bioinformatics genome-annotation genomics gff3 python


BEDMatrix : A matrix-like wrapper around PLINK .bed files
author: QuantGen
created: 2015-05-21 19:29:11
bed cran genetics genomics ped plink r r-pkg


stackr : stackr: an R package to run stacks software pipeline
author: thierrygosselin
created: 2015-05-23 03:21:36
filter gbs genetics genomic-data-analysis genomics genomics-visualization genotype-likelihoods genotyping-by-sequencing rad radseq radseq-data stackr r


transit : Repository for the TRANSIT and TPP tools developed by the Ioerger Lab
author: mad-lab
created: 2015-05-23 17:38:34
analysis essentiality genomes genomics mutagenesis tn-seq tnseq transposon python


QuantumClone : Clonal reconstruction from HTS data
author: DeveauP
created: 2015-07-06 11:17:43
analysis clustering cran genomics oncology r


TaFuCo : Targeted Fusion Caller (C)
author: r3fang
created: 2015-07-07 19:54:38
bioinformatics fusion gene genomics illumina rna-seq transcript c


Cookies help us deliver our services. By using our services, you agree to our use of cookies Learn more