spades by ablab

SPAdes Genome Assembler

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

32 +1

668 +5

131 +0

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

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

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

cufflinks by cole-trapnell-lab

None

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

36 +0

301 +0

115 +0

mummer by mummer4

Mummer alignment tool

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

20 +0

420 +1

108 +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

104 +1

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

wgsim by lh3

Reads simulator

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

17 +0

248 +0

89 +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

bedtools by arq5x

A powerful toolset for genome arithmetic.

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

20 +0

140 +1

87 +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

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 +0

83 +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

FastQC by s-andrews

A quality control analysis tool for high throughput sequencing data

created at Dec. 21, 2017, 11:48 a.m.

13 +1

393 +5

79 +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

gffutils by daler

GFF and GTF file manipulation and interconversion

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

14 +0

267 +0

74 +0

SnpEff by pcingola

None

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

25 +1

230 +2

74 +0

pyfaidx by mdshw5

Efficient pythonic random access to fasta subsequences

created at Sept. 12, 2013, 7:02 p.m.

9 +0

440 +0

73 +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