diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

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

38 +0

1,078 +5

181 -1

freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

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

46 +0

792 +1

265 +0

spades by ablab

SPAdes Genome Assembler

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

32 +0

769 +3

139 +0

bowtie2 by BenLangmead

A fast and sensitive gapped read aligner

created at Dec. 20, 2012, 7:25 p.m.

32 +0

684 +1

159 +0

canu by marbl

A single molecule sequence assembler for genomes large and small.

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

54 +0

661 +0

179 +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.

40 +0

628 +3

221 +0

hifiasm by chhylp123

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

30 +0

559 +3

88 +0

vcftools by vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

created at June 25, 2015, 1:48 p.m.

32 +0

506 +1

148 +0

mummer by mummer4

Mummer alignment tool

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

21 +0

473 +1

108 +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

448 +2

138 +1

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

424 +3

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

420 +0

153 +0

manta by Illumina

Structural variant and indel caller for mapped sequencing data

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

41 +0

415 +0

154 +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.

25 +0

414 +1

82 +0

cufflinks by cole-trapnell-lab

None

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

36 +0

312 +0

116 +0

octopus by luntergroup

Bayesian haplotype-based mutation calling

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

19 +0

305 +0

37 +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

154 +0

39 +0

bedtools by arq5x

A powerful toolset for genome arithmetic.

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

20 +0

140 +0

85 +0

SKESA by ncbi

SKESA assembler

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

17 +0

112 +0

19 +0

telseq by zd1

A software for calculating telomere length

created at May 27, 2013, 3:58 p.m.

9 +0

67 +0

26 +0