tabix by samtools

Note: tabix and bgzip binaries are now part of the HTSlib project.

created at March 9, 2012, 1:46 a.m.

22 +0

91 +0

40 +0

RSEM by deweylab

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

created at Feb. 9, 2011, 5:30 a.m.

22 -1

397 +2

118 +1

mummer by mummer4

Mummer alignment tool

created at July 23, 2015, 5:33 p.m.

20 -1

419 +4

108 +0

pileup.js by hammerlab

Interactive in-browser track viewer

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

20 +0

272 +1

66 +0

bedtools by arq5x

A powerful toolset for genome arithmetic.

created at Jan. 3, 2011, 2:43 a.m.

20 +0

139 +0

87 +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

octopus by luntergroup

Bayesian haplotype-based mutation calling

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

19 +0

296 +0

37 +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

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

fastx_toolkit by agordon

FASTA/FASTQ pre-processing programs

created at Nov. 8, 2013, 1:03 p.m.

18 +0

155 +0

60 +0

parasail by jeffdaily

Pairwise Sequence Alignment Library

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

18 +0

233 +1

34 +0

bioSyntax by bioSyntax

Syntax highlighting for computational biology

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

17 +0

247 +2

30 +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

wgsim by lh3

Reads simulator

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

17 +0

248 +0

89 +0

cruzdb by brentp

python access to UCSC genomes database

created at Sept. 2, 2011, 3:36 p.m.

17 +0

134 +1

41 +0

SKESA by ncbi

SKESA assembler

created at July 11, 2018, 8:13 p.m.

17 +1

104 +1

16 +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

GLnexus by dnanexus-rnd

Scalable gVCF merging and joint variant calling for population sequencing projects

created at April 8, 2015, 5:05 a.m.

15 +0

133 +1

35 +0

biocaml by biocaml

OCaml Bioinformatics Library

created at March 22, 2010, 10:08 p.m.

15 +0

121 +0

21 +0

redun by insitro

Yet another redundant workflow engine

created at Nov. 4, 2021, 12:14 a.m.

15 +0

486 +2

37 +0