bamtools by pezmaster31

C++ API & command-line toolkit for working with BAM data

updated at May 18, 2024, 9:46 a.m.

27 +0

410 +1

153 +0

octopus by luntergroup

Bayesian haplotype-based mutation calling

updated at May 17, 2024, 11:29 p.m.

19 +0

297 +1

37 +0

vcflib by vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

updated at May 17, 2024, 7:41 a.m.

39 +0

604 +5

219 +0

bowtie2 by BenLangmead

A fast and sensitive gapped read aligner

updated at May 17, 2024, 2:58 a.m.

30 +0

623 +1

162 +0

diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

updated at May 17, 2024, 1:18 a.m.

36 +0

966 +2

172 +1

RSEM by deweylab

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

updated at May 16, 2024, 9:06 a.m.

22 +0

399 +1

118 +0

spades by ablab

SPAdes Genome Assembler

updated at May 15, 2024, 2:48 p.m.

32 +0

677 +1

131 +0

freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

updated at May 15, 2024, 7:57 a.m.

46 +0

749 +1

259 +0

hifiasm by chhylp123

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

updated at May 13, 2024, 3:43 p.m.

29 +0

483 +2

82 +4

mummer by mummer4

Mummer alignment tool

updated at May 13, 2024, 7:30 a.m.

20 +0

424 +1

109 +0

cufflinks by cole-trapnell-lab

None

updated at May 12, 2024, 12:55 p.m.

36 +0

302 +1

115 +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.

updated at May 11, 2024, 2:58 p.m.

32 +0

480 +0

147 +0

telseq by zd1

A software for calculating telomere length

updated at May 11, 2024, 7:13 a.m.

9 +0

64 +0

26 +0

delly by dellytools

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

updated at May 10, 2024, 8:20 a.m.

34 +0

403 +0

136 +0

SKESA by ncbi

SKESA assembler

updated at May 9, 2024, 5:03 a.m.

17 +0

105 +0

16 +0

canu by marbl

A single molecule sequence assembler for genomes large and small.

updated at May 8, 2024, 2:52 p.m.

54 +0

632 +0

177 +0

seqan3 by seqan

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

updated at May 7, 2024, 9:11 a.m.

24 +0

389 +0

80 +0

GLnexus by dnanexus-rnd

Scalable gVCF merging and joint variant calling for population sequencing projects

updated at May 5, 2024, 5:51 a.m.

15 +0

135 +0

35 +0

bedtools by arq5x

A powerful toolset for genome arithmetic.

updated at May 1, 2024, 8:58 a.m.

20 +0

140 +0

87 +0

manta by Illumina

Structural variant and indel caller for mapped sequencing data

updated at April 20, 2024, 3:14 p.m.

41 +0

388 +0

151 +0