awesome-pipeline by pditommaso

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

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

234 +0

5,928 +16

616 +0

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.

128 -2

5,823 +6

603 +2

bioinformatics by ossu

Path to a free self-taught education in Bioinformatics!

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

358 +0

5,045 +26

855 +7

biopython by biopython

Official git repository for Biopython (originally converted from CVS)

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

168 -2

4,175 +6

1,714 +2

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.

159 -1

3,080 +3

695 +0

nextflow by nextflow-io

A DSL for data-driven computational pipelines

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

86 +0

2,547 +7

592 +2

oneliners by stephenturner

Useful bash one-liners for bioinformatics.

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

157 +0

1,803 +1

511 +0

samtools by samtools

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

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

100 -1

1,552 +3

570 +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

1,512 +5

199 +0

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.

107 +0

1,454 +1

544 +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

1,441 +0

199 +0

seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

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

62 +0

1,313 +1

308 +1

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.

184 +0

1,312 +2

616 +1

MMseqs2 by soedinglab

MMseqs2: ultra fast and sensitive search and clustering suite

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

31 +0

1,261 +5

179 +0

seqkit by shenwei356

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

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

27 +0

1,207 +3

156 +0

MultiQC by MultiQC

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

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

37 +1

1,174 +7

580 +1

scipipe by scipipe

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

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

38 +0

1,053 -1

72 +0

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.

87 +0

974 +1

357 +0

diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

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

36 -1

961 +3

170 +1

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.

112 +0

960 +2

350 +1