diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

created at March 10, 2015, 11:19 p.m.

C++

37 +0

942 +3

170 +1

GitHub
hail by hail-is

Cloud-native genomic dataframes and batch computing

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

Python

56 +0

927 +1

236 +1

GitHub
bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

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

C

58 +0

888 +3

282 -3

GitHub
RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

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

Python

78 +0

821 +6

287 +0

GitHub
prokka by tseemann

zap aquarius Rapid prokaryotic genome annotation

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

Perl

43 +0

748 +4

214 +1

GitHub
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.

Cython

48 +0

743 +3

268 -1

GitHub
freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

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

C++

48 +0

742 +3

258 +0

GitHub
Flye by fenderglass

De novo assembler for single molecule sequencing reads using repeat graphs

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

C

28 +0

714 +3

160 +1

GitHub
ChIP-seq-analysis by crazyhottommy

ChIP-seq analysis notes from Ming Tang

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

Python

65 +0

692 +4

286 +0

GitHub
spades by ablab

SPAdes Genome Assembler

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

C++

32 +0

653 +2

131 +0

GitHub
mosdepth by brentp

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

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

Nim

24 +0

644 +4

99 +0

GitHub
poly by bebop

A Go package for engineering organisms.

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

Go

12 +0

641 +3

67 +0

GitHub
canu by marbl

A single molecule sequence assembler for genomes large and small.

created at Aug. 21, 2015, 3:10 a.m.

C++

54 +0

626 +3

177 +0

GitHub
zindex by mattgodbolt

Create an index on a compressed text file

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

C

23 +0

613 +0

41 +0

GitHub
bowtie2 by BenLangmead

A fast and sensitive gapped read aligner

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

C++

30 +0

613 +2

160 +1

GitHub
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.

C

48 +0

610 +5

231 +0

GitHub
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.

Java

50 +0

606 +3

376 +1

GitHub
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.

C++

39 +0

590 +2

218 -1

GitHub
wtdbg2 by ruanjue

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

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

C

32 +0

490 +2

89 +0

GitHub
biojs by biojs

🔬A library of JavaScript components to represent biological data

created at Aug. 2, 2013, 3:05 p.m.

Unknown languages

70 +0

482 +1

121 +0

GitHub