nextflow by nextflow-io

A DSL for data-driven computational pipelines

created at March 27, 2013, 11:17 a.m.

86 -1

2,539 +3

588 +4

seqmagick by fhcrc

An imagemagick-like frontend to Biopython SeqIO

created at Nov. 24, 2010, 12:48 a.m.

12 +0

108 +0

22 +0

fastx_toolkit by agordon

FASTA/FASTQ pre-processing programs

created at Nov. 8, 2013, 1:03 p.m.

18 +0

155 +0

60 +0

sra-explorer by ewels

Web application to explore the Sequence Read Archive.

created at Sept. 19, 2014, 8:15 a.m.

9 +0

188 +2

27 +0

common-workflow-language by common-workflow-language

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

created at Sept. 25, 2014, 11:04 a.m.

112 +0

1,440 +1

199 +0

BigDataScript by pcingola

BigDataScript: Scirpting language for big data

created at March 3, 2013, 6 p.m.

13 +0

93 +1

21 +0

gatk by broadgsa

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

created at June 28, 2011, 1:08 p.m.

68 +0

293 +0

221 +0

r-peridot by pentalpha

Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.

created at April 27, 2017, 5:47 p.m.

2 +0

4 +0

0 +0

fujiplot by mkanai

Fuji plot—a circos representation of multiple GWAS results—

created at Feb. 10, 2018, 12:23 p.m.

3 +0

65 +1

19 +0

cufflinks by cole-trapnell-lab

None

created at July 25, 2014, 10:42 p.m.

36 +0

300 +0

115 +0

parasail by jeffdaily

Pairwise Sequence Alignment Library

created at May 21, 2015, 7:31 p.m.

18 +0

232 +1

34 +0

mummer by mummer4

Mummer alignment tool

created at July 23, 2015, 5:33 p.m.

21 +0

415 +1

108 +0

seqan3 by seqan

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

created at April 4, 2016, 12:39 p.m.

24 +0

387 +2

80 +0

rust-bio by rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

created at Jan. 25, 2015, 4:40 p.m.

70 +0

1,496 +8

197 +0

RSEM by deweylab

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

created at Feb. 9, 2011, 5:30 a.m.

23 +0

395 +1

117 +0

poapy by ljdursi

A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes

created at April 28, 2015, 9:38 p.m.

8 +0

68 +1

12 +0

freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

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

46 +0

744 +1

259 +1

deepvariant by google

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

created at Nov. 23, 2017, 1:56 a.m.

160 +0

3,076 +6

694 -1

MMseqs2 by soedinglab

MMseqs2: ultra fast and sensitive search and clustering suite

created at July 20, 2016, 6:17 a.m.

31 -1

1,247 +6

179 +2

octopus by luntergroup

Bayesian haplotype-based mutation calling

created at Feb. 4, 2015, 9:24 a.m.

19 +0

296 +0

37 +0