bioinformatics by ossu

Path to a free self-taught education in Bioinformatics!

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

359 +1

5,057 +12

856 +1

awesome-pipeline by pditommaso

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

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

235 +1

5,937 +9

616 +0

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 +0

616 +0

biopython by biopython

Official git repository for Biopython (originally converted from CVS)

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

168 +0

4,181 +6

1,717 +3

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 +0

3,084 +4

696 +1

oneliners by stephenturner

Useful bash one-liners for bioinformatics.

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

157 +0

1,804 +1

511 +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 +0

5,833 +10

603 +0

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

959 -1

350 +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

1,442 +1

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 +0

544 +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 +0

1,556 +4

571 +1

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

975 +1

357 +0

nextflow by nextflow-io

A DSL for data-driven computational pipelines

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

85 -1

2,555 +8

593 +1

RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

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

78 +0

840 +1

290 +0

sift by teamdfir

SIFT

created at Jan. 18, 2014, 7:20 p.m.

74 +0

470 +0

66 +0

biojs by biojs

🔬A library of JavaScript components to represent biological data

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

70 +0

484 +0

121 +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

1,517 +5

199 +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

222 +0

ChIP-seq-analysis by crazyhottommy

ChIP-seq analysis notes from Ming Tang

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

65 +0

709 +1

290 +0

seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

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

62 +0

1,316 +3

308 +0