SnpEff by pcingola

None

created at Jan. 31, 2014, 10:22 p.m.

24 +0

227 +0

74 +0

wgsim by lh3

Reads simulator

created at Jan. 22, 2011, 10:57 p.m.

17 +0

248 +0

89 +0

bamsurgeon by adamewing

tools for adding mutations to existing .bam files, used for testing mutation callers

created at May 10, 2012, 10:18 p.m.

15 +0

225 +0

83 +0

bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

created at Dec. 9, 2013, 9:18 p.m.

58 +0

898 +2

282 +0

gffutils by daler

GFF and GTF file manipulation and interconversion

created at Oct. 12, 2011, 1:48 p.m.

14 +0

265 +1

74 +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

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

vcfanno by brentp

annotate a VCF with other VCFs/BEDs/tabixed files

created at April 29, 2015, 4 p.m.

26 +0

346 +1

55 +0

bcftools by samtools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

created at July 12, 2013, 12:55 p.m.

48 +0

619 +0

236 +2

telseq by zd1

A software for calculating telomere length

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

9 +0

62 +0

26 +0

samstat by TimoLassmann

SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.

created at Dec. 11, 2017, 7:07 a.m.

3 +0

23 +0

7 +0

mergesam by DarwinAwardWinner

Automate common sam & bam conversions

created at Aug. 26, 2011, 2:19 p.m.

3 +0

6 +0

1 +0

bam-toolbox by AndersenLab

A bam toolbox

created at Oct. 28, 2015, 4:36 p.m.

10 +0

1 +0

1 +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

bwa by lh3

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

created at Jan. 14, 2011, 1:36 a.m.

106 +0

1,443 +2

542 +2

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

seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

created at March 23, 2012, 11:24 p.m.

62 +0

1,310 +2

306 +0

seqkit by shenwei356

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

created at Feb. 28, 2016, 10:04 a.m.

27 +0

1,201 +7

154 +0

fastqp by mdshw5

Simple FASTQ quality assessment using Python

created at Sept. 23, 2013, 8:01 p.m.

6 +0

107 +0

14 +0

bcbio-nextgen by bcbio

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

created at Feb. 6, 2013, 11:14 a.m.

87 +0

974 +1

357 +0