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 +0

398 +1

118 +0

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

pyensembl by openvax

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

created at April 14, 2014, 3:23 p.m.

22 +0

353 +1

66 +0

mosdepth by brentp

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

created at Aug. 24, 2017, 4:32 p.m.

23 +0

657 +2

100 +0

zindex by mattgodbolt

Create an index on a compressed text file

created at Feb. 26, 2015, 1:33 p.m.

23 +0

613 -1

41 +0

seqan3 by seqan

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

created at April 4, 2016, 12:39 p.m.

24 +0

389 +0

80 +0

gridss by PapenfussLab

GRIDSS: the Genomic Rearrangement IDentification Software Suite

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

24 +0

244 +1

73 +0

csvtk by shenwei356

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

created at April 3, 2016, 2:31 p.m.

25 +0

956 +1

84 +0

SnpEff by pcingola

None

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

25 +1

230 +2

74 +0

vcfanno by brentp

annotate a VCF with other VCFs/BEDs/tabixed files

created at April 29, 2015, 4 p.m.

26 +0

348 +0

55 +0

seqware by SeqWare

This is the SeqWare Project's main repo.

created at May 11, 2012, 3:51 p.m.

26 +0

28 +0

17 +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

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 +0

118 +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

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

hifiasm by chhylp123

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

created at May 9, 2019, 7:34 p.m.

29 +0

475 +3

78 +1

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

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

wtdbg2 by ruanjue

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

created at Sept. 29, 2017, 10:24 a.m.

31 +0

493 +0

89 +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