bamtools by pezmaster31

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

updated at March 22, 2024, 8 a.m.

27 +0

408 +0

153 +0

octopus by luntergroup

Bayesian haplotype-based mutation calling

updated at April 13, 2024, 5:26 a.m.

19 +0

296 +0

37 +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

SKESA by ncbi

SKESA assembler

updated at April 21, 2024, 1:56 p.m.

17 +0

104 +0

16 +0

cufflinks by cole-trapnell-lab

None

updated at April 25, 2024, 3:01 p.m.

36 +0

301 +0

115 +0

seqan3 by seqan

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

updated at April 26, 2024, 1:20 a.m.

24 +0

389 +0

80 +0

telseq by zd1

A software for calculating telomere length

updated at April 26, 2024, 7:04 p.m.

9 +0

63 +0

26 +0

canu by marbl

A single molecule sequence assembler for genomes large and small.

updated at April 28, 2024, 1:58 p.m.

54 +0

631 +1

177 +0

mummer by mummer4

Mummer alignment tool

updated at May 1, 2024, 7:32 a.m.

20 +0

420 +1

108 +0

bedtools by arq5x

A powerful toolset for genome arithmetic.

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

20 +0

140 +1

87 +0

freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

updated at May 1, 2024, 9:52 a.m.

46 +0

747 +1

259 +0

delly by dellytools

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

updated at May 1, 2024, 3:27 p.m.

34 +0

401 +1

136 +1

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 1, 2024, 3:51 p.m.

32 +0

476 -1

147 +0

bowtie2 by BenLangmead

A fast and sensitive gapped read aligner

updated at May 1, 2024, 11:03 p.m.

30 +0

621 +2

162 +0

hifiasm by chhylp123

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

29 +0

475 +3

78 +1

diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

updated at May 2, 2024, 5:29 p.m.

36 -1

961 +3

170 +1

vcflib by vcflib

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

updated at May 3, 2024, 8:53 p.m.

39 +0

598 +2

219 +1

spades by ablab

SPAdes Genome Assembler

updated at May 5, 2024, 1:48 a.m.

32 +1

668 +5

131 +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 +2

35 +0

RSEM by deweylab

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

updated at May 5, 2024, 8:28 a.m.

22 +0

398 +1

118 +0