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

136 +0

4,642 +2

550 +1

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

219 +0

4,116 +15

464 +1

GitHub
biopython by biopython

Official git repository for Biopython (originally converted from CVS)

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

Python

164 -1

2,798 +7

1,345 +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

164 -2

2,308 +9

572 +0

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

240 +2

2,095 +18

436 +4

GitHub
nextflow by nextflow-io

A DSL for data-driven computational pipelines

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

Groovy

82 +0

1,438 +1

353 +1

GitHub
oneliners by stephenturner

Useful bash one-liners for bioinformatics.

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

Unknown languages

142 +0

1,296 +4

402 +2

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.

Python

116 +0

1,259 +1

181 +0

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

102 +0

1,100 +0

473 +0

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

1,079 +3

559 +1

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 +1

1,013 -1

487 +1

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

66 +0

939 +6

138 +1

GitHub
seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

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

C

62 +0

851 +5

249 +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

91 +0

822 +0

339 +0

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

39 +0

753 +2

409 +1

GitHub
hail by hail-is

Scalable genomic data analysis.

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

Python

60 +0

737 +2

198 +0

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

104 +0

712 +0

243 +1

GitHub
bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

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

C

57 +0

700 +2

253 +0

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

29 +0

661 +2

100 +1

GitHub
csvtk by shenwei356

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

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

Go

21 +0

624 +2

63 +0

GitHub