bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

created at Dec. 9, 2013, 9:18 p.m.

58 +0

905 +1

285 +0

hail by hail-is

Cloud-native genomic dataframes and batch computing

created at Oct. 27, 2015, 8:55 p.m.

55 +0

943 +2

238 +2

canu by marbl

A single molecule sequence assembler for genomes large and small.

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

54 +0

634 +2

176 -1

bioperl-live by bioperl

Core BioPerl 1.x code

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

54 +0

289 +1

178 +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.

52 +1

458 +1

198 +1

igv by igvteam

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

created at Feb. 11, 2012, 5:30 p.m.

50 +0

614 +1

377 +0

bcftools by samtools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

created at July 12, 2013, 12:55 p.m.

49 +0

623 +1

241 +1

pysam by pysam-developers

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

created at Feb. 5, 2014, 8:38 p.m.

48 +0

754 +2

271 +0

AGAT by NBISweden

Another Gtf/Gff Analysis Toolkit

created at Nov. 19, 2019, 9:35 a.m.

47 +1

419 +4

52 +0

freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

created at Oct. 13, 2010, 9:34 p.m.

46 +0

751 +2

259 +0

prokka by tseemann

Rapid prokaryotic genome annotation

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

45 +0

766 +6

218 +0

manta by Illumina

Structural variant and indel caller for mapped sequencing data

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

41 +0

389 +1

151 +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

603 -1

219 +0

scipipe by scipipe

Robust, flexible and resource-efficient pipelines using Go and the commandline

created at March 7, 2015, 9:47 p.m.

38 +0

1,055 +1

72 +0

MultiQC by MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

created at Aug. 4, 2015, 1:47 p.m.

37 +0

1,178 +1

581 +0

bionode by bionode

Modular and universal bioinformatics

created at Jan. 23, 2014, 11:56 p.m.

36 +0

308 +0

39 +0

diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

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

36 +0

972 +6

173 +1

cufflinks by cole-trapnell-lab

None

created at July 25, 2014, 10:42 p.m.

36 +0

302 +0

115 +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

406 +3

136 +0

dalliance by dasmoth

Interactive web-based genome browser.

created at July 1, 2010, 6:29 p.m.

34 +0

226 +0

68 +0