csvkit by wireservice

A suite of utilities for converting to and working with CSV, the king of tabular file formats.

created at April 1, 2011, 3 a.m.

Python

133 +0

5,063 +8

582 +0

GitHub
awesome-pipeline by pditommaso

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

created at July 19, 2014, 3:48 p.m.

Unknown languages

224 +1

4,963 +10

523 +2

GitHub
biopython by biopython

Official git repository for Biopython (originally converted from CVS)

created at March 15, 2009, 9:09 p.m.

Python

163 +0

3,195 +7

1,501 +2

GitHub
bioinformatics by ossu

microscope Path to a free self-taught education in Bioinformatics!

created at June 21, 2016, 11:11 p.m.

Unknown languages

289 +4

2,862 +15

572 +6

GitHub
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.

Python

162 +0

2,551 +6

639 +0

GitHub
nextflow by nextflow-io

A DSL for data-driven computational pipelines

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

Groovy

79 +0

1,796 +3

466 +3

GitHub
oneliners by stephenturner

Useful bash one-liners for bioinformatics.

created at Oct. 19, 2013, 11:33 a.m.

Unknown languages

152 +0

1,550 +2

462 +0

GitHub
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.

Common Workflow Language

118 +0

1,352 +1

201 -1

GitHub
samtools by samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

created at March 9, 2012, 2:49 a.m.

C

98 +0

1,231 +3

511 +1

GitHub
rnaseq_tutorial by griffithlab

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

created at July 31, 2014, 6:58 p.m.

R

187 +0

1,174 -1

597 +2

GitHub
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.

C

110 +0

1,164 +4

517 +0

GitHub
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.

Rust

70 +0

1,126 +2

164 +0

GitHub
seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

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

C

59 +0

1,006 +4

283 +0

GitHub
scipipe by scipipe

Robust, flexible and resource-efficient pipelines using Go and the commandline

created at March 7, 2015, 9:47 p.m.

Go

37 +0

951 +8

68 +1

GitHub
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.

Python

88 +0

884 -1

349 -1

GitHub
seqkit by shenwei356

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

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

Go

27 +0

878 +5

128 +1

GitHub
MultiQC by ewels

Aggregate results from bioinformatics analyses across many samples into a single report.

created at Aug. 4, 2015, 1:47 p.m.

Python

38 +0

866 +1

479 +1

GitHub
cromwell by broadinstitute

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

created at April 17, 2015, 7:39 p.m.

Scala

110 -1

824 +2

291 +0

GitHub
hail by hail-is

Scalable genomic data analysis.

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

Python

58 +0

813 -1

218 +0

GitHub
bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

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

C

59 +0

769 +2

270 +0

GitHub