biopython by biopython

Official git repository for Biopython (originally converted from CVS)

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

170 -1

4,160 +12

1,711 +2

bioinformatics by ossu

Path to a free self-taught education in Bioinformatics!

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

357 +1

5,001 +9

842 +0

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

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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

5,904 +9

615 +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 -1

1,310 +1

615 +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.

131 +0

5,812 +4

600 +0

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

MultiQC by MultiQC

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

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

36 +0

1,163 +2

578 +2

samtools by samtools

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

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

101 +0

1,546 +3

569 +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.

106 +0

1,443 +2

542 +2

oneliners by stephenturner

Useful bash one-liners for bioinformatics.

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

157 -1

1,800 +6

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igv by igvteam

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

created at Feb. 11, 2012, 5:30 p.m.

50 +0

609 +0

376 +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

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.

113 +0

957 +4

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seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

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

62 +0

1,310 +2

306 +0

RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

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

78 +0

835 +1

290 +1

ChIP-seq-analysis by crazyhottommy

ChIP-seq analysis notes from Ming Tang

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

65 +0

702 +3

288 +0

bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

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

58 +0

898 +2

282 +0

pysam by pysam-developers

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

created at Feb. 5, 2014, 8:38 p.m.

48 +0

750 +0

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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