biojs by biojs

🔬A library of JavaScript components to represent biological data

created at Aug. 2, 2013, 3:05 p.m.

70 +0

484 +0

121 +0

spades by ablab

SPAdes Genome Assembler

created at June 1, 2016, 3:06 p.m.

32 +1

668 +5

131 +0

delly by dellytools

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

created at Nov. 15, 2013, 8:51 a.m.

34 +0

401 +1

136 +1

vcftools by vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

created at June 25, 2015, 1:48 p.m.

32 +0

476 -1

147 +0

manta by Illumina

Structural variant and indel caller for mapped sequencing data

created at May 30, 2013, 7:33 p.m.

41 +0

388 +0

151 +0

bamtools by pezmaster31

C++ API & command-line toolkit for working with BAM data

created at May 21, 2010, 7:35 p.m.

27 +0

408 +0

153 +0

seqkit by shenwei356

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

created at Feb. 28, 2016, 10:04 a.m.

27 +0

1,207 +3

156 +0

Flye by fenderglass

De novo assembler for single molecule sequencing reads using repeat graphs

created at March 17, 2016, 10:47 p.m.

28 +0

728 +2

160 +0

bowtie2 by BenLangmead

A fast and sensitive gapped read aligner

created at Dec. 20, 2012, 7:25 p.m.

30 +0

621 +2

162 +0

diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

created at March 10, 2015, 11:19 p.m.

36 -1

961 +3

170 +1

canu by marbl

A single molecule sequence assembler for genomes large and small.

created at Aug. 21, 2015, 3:10 a.m.

54 +0

631 +1

177 +0

bioperl-live by bioperl

Core BioPerl 1.x code

created at May 12, 2010, 5:13 p.m.

54 +0

289 +0

178 +0

MMseqs2 by soedinglab

MMseqs2: ultra fast and sensitive search and clustering suite

created at July 20, 2016, 6:17 a.m.

31 +0

1,261 +5

179 +0

jbrowse by GMOD

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

created at Jan. 16, 2009, 11:30 a.m.

51 +0

457 +0

197 +0

rust-bio by rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

created at Jan. 25, 2015, 4:40 p.m.

70 +0

1,512 +5

199 +0

common-workflow-language by common-workflow-language

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

created at Sept. 25, 2014, 11:04 a.m.

112 +0

1,441 +0

199 +0

PyVCF by jamescasbon

A Variant Call Format reader for Python.

created at Oct. 30, 2011, 4:52 p.m.

31 +0

392 +0

199 +0

prokka by tseemann

Rapid prokaryotic genome annotation

created at March 26, 2014, 7:19 a.m.

44 +1

758 +4

216 +0

vcflib by vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

created at Sept. 22, 2010, 11:25 p.m.

39 +0

598 +2

219 +1

gatk by broadgsa

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

created at June 28, 2011, 1:08 p.m.

68 +0

293 +0

222 +0