diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

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

37 +0

954 +3

170 +1

freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

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

46 +0

744 +1

259 +1

spades by ablab

SPAdes Genome Assembler

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

31 -1

658 -1

131 +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

629 +0

177 +0

bowtie2 by BenLangmead

A fast and sensitive gapped read aligner

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

30 +0

617 +2

162 +1

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.

39 +0

593 +1

217 +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

475 +0

147 +1

hifiasm by chhylp123

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

29 +0

472 +0

77 +0

mummer by mummer4

Mummer alignment tool

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

21 +0

415 +1

108 +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

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

399 +1

135 +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.

23 +0

395 +1

117 +0

manta by Illumina

Structural variant and indel caller for mapped sequencing data

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

41 +0

388 +2

150 +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

387 +2

80 +0

cufflinks by cole-trapnell-lab

None

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

36 +0

300 +0

115 +0

octopus by luntergroup

Bayesian haplotype-based mutation calling

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

19 +0

296 +0

37 +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

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

132 +1

35 +0

SKESA by ncbi

SKESA assembler

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

16 +0

103 +2

16 +0

telseq by zd1

A software for calculating telomere length

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

9 +0

62 +0

26 +0