freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

updated at April 28, 2024, 5:53 a.m.

46 +0

746 +2

259 +0

canu by marbl

A single molecule sequence assembler for genomes large and small.

updated at April 28, 2024, 3:15 a.m.

54 +0

630 +1

177 +0

GLnexus by dnanexus-rnd

Scalable gVCF merging and joint variant calling for population sequencing projects

updated at April 27, 2024, 2:06 p.m.

15 +0

133 +1

35 +0

hifiasm by chhylp123

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

updated at April 27, 2024, 11:59 a.m.

29 +0

472 +0

77 +0

mummer by mummer4

Mummer alignment tool

updated at April 26, 2024, 7:59 p.m.

20 -1

419 +4

108 +0

telseq by zd1

A software for calculating telomere length

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

9 +0

63 +1

26 +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 April 26, 2024, 4:31 p.m.

32 +0

477 +2

147 +0

spades by ablab

SPAdes Genome Assembler

updated at April 26, 2024, 4:24 p.m.

31 +0

663 +5

131 +0

delly by dellytools

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

updated at April 26, 2024, 12:25 p.m.

34 +0

400 +1

135 +0

vcflib by vcflib

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

updated at April 26, 2024, 11:58 a.m.

39 +0

596 +3

218 +1

bowtie2 by BenLangmead

A fast and sensitive gapped read aligner

updated at April 26, 2024, 6:07 a.m.

30 +0

619 +2

162 +0

RSEM by deweylab

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

updated at April 26, 2024, 4:44 a.m.

22 -1

397 +2

118 +1

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 +2

80 +0

diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

updated at April 25, 2024, 9:47 p.m.

37 +0

958 +4

169 -1

cufflinks by cole-trapnell-lab

None

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

36 +0

301 +1

115 +0

SKESA by ncbi

SKESA assembler

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

17 +1

104 +1

16 +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 +1

octopus by luntergroup

Bayesian haplotype-based mutation calling

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

19 +0

296 +0

37 +0

bedtools by arq5x

A powerful toolset for genome arithmetic.

updated at April 12, 2024, 10:03 a.m.

20 +0

139 +0

87 +0

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