cufflinks by cole-trapnell-lab

None

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

36 +0

301 +1

115 +0

lumpy-sv by arq5x

lumpy: a general probabilistic framework for structural variant discovery

created at Oct. 8, 2012, 9:09 a.m.

27 +0

299 +1

118 +0

octopus by luntergroup

Bayesian haplotype-based mutation calling

created at Feb. 4, 2015, 9:24 a.m.

19 +0

296 +0

37 +0

pybedtools by daler

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

created at May 14, 2010, 9:09 p.m.

17 +0

293 +0

103 +0

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 +1

bioperl-live by bioperl

Core BioPerl 1.x code

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

54 +0

289 +0

178 +1

pileup.js by hammerlab

Interactive in-browser track viewer

created at Jan. 27, 2015, 8:36 p.m.

20 +0

272 +1

66 +0

bioservices by cokelaer

Access to Biological Web Services from Python.

created at Aug. 28, 2014, 3:24 p.m.

18 +0

271 +0

61 +0

gffutils by daler

GFF and GTF file manipulation and interconversion

created at Oct. 12, 2011, 1:48 p.m.

14 +0

267 +2

74 +0

somalier by brentp

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

created at Aug. 7, 2018, 2:52 p.m.

11 +0

253 +0

35 +0

wgsim by lh3

Reads simulator

created at Jan. 22, 2011, 10:57 p.m.

17 +0

248 +0

89 +0

bioSyntax by bioSyntax

Syntax highlighting for computational biology

created at Dec. 5, 2017, 2:25 a.m.

17 +0

247 +2

30 +0

gridss by PapenfussLab

GRIDSS: the Genomic Rearrangement IDentification Software Suite

created at June 11, 2015, 11 a.m.

24 +0

243 +1

73 +0

parasail by jeffdaily

Pairwise Sequence Alignment Library

created at May 21, 2015, 7:31 p.m.

18 +0

233 +1

34 +0

SnpEff by pcingola

None

created at Jan. 31, 2014, 10:22 p.m.

24 +0

228 +1

74 +0

dalliance by dasmoth

Interactive web-based genome browser.

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

34 +0

226 +0

68 +0

bamsurgeon by adamewing

tools for adding mutations to existing .bam files, used for testing mutation callers

created at May 10, 2012, 10:18 p.m.

15 +0

226 +1

83 +0

bpipe by ssadedin

Bpipe - a tool for running and managing bioinformatics pipelines

created at Oct. 20, 2014, 4:31 a.m.

19 +0

223 +0

56 +0

smoove by brentp

structural variant calling and genotyping with existing tools, but, smoothly.

created at Jan. 27, 2018, 3:03 a.m.

10 +0

219 +0

21 +0

AfterQC by OpenGene

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

created at Aug. 4, 2015, 2:08 p.m.

20 +0

201 +0

51 +0