csvtk by shenwei356

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

created at April 3, 2016, 2:31 p.m.

25 +0

955 +4

84 +0

hail by hail-is

Cloud-native genomic dataframes and batch computing

created at Oct. 27, 2015, 8:55 p.m.

55 +0

934 -2

235 +1

bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

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

58 +0

898 +0

283 +1

RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

created at Aug. 26, 2015, 7:37 p.m.

78 +0

839 +4

290 +0

prokka by tseemann

Rapid prokaryotic genome annotation

created at March 26, 2014, 7:19 a.m.

43 +0

754 +4

216 +1

pysam by pysam-developers

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

created at Feb. 5, 2014, 8:38 p.m.

48 +0

749 -1

270 +1

freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

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

46 +0

746 +2

259 +0

Flye by fenderglass

De novo assembler for single molecule sequencing reads using repeat graphs

created at March 17, 2016, 10:47 p.m.

28 +0

726 +1

160 +1

ChIP-seq-analysis by crazyhottommy

ChIP-seq analysis notes from Ming Tang

created at June 12, 2015, 9:42 p.m.

65 +0

708 +6

290 +2

spades by ablab

SPAdes Genome Assembler

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

31 +0

663 +5

131 +0

mosdepth by brentp

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

created at Aug. 24, 2017, 4:32 p.m.

23 +0

655 +2

100 +0

poly by bebop

A Go package for engineering organisms.

created at May 29, 2020, 9 p.m.

12 +0

649 +1

68 +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

630 +1

177 +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

620 +1

237 +1

bowtie2 by BenLangmead

A fast and sensitive gapped read aligner

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

30 +0

619 +2

162 +0

zindex by mattgodbolt

Create an index on a compressed text file

created at Feb. 26, 2015, 1:33 p.m.

23 +0

614 +1

41 +0

igv by igvteam

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

created at Feb. 11, 2012, 5:30 p.m.

50 +0

609 +0

377 +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

596 +3

218 +1

wtdbg2 by ruanjue

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

created at Sept. 29, 2017, 10:24 a.m.

31 -1

493 +1

89 +0

redun by insitro

Yet another redundant workflow engine

created at Nov. 4, 2021, 12:14 a.m.

15 +0

486 +2

37 +0