biopython by biopython

Official git repository for Biopython (originally converted from CVS)

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

170 +0

4,169 +9

1,712 +1

bioinformatics by ossu

Path to a free self-taught education in Bioinformatics!

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

358 +1

5,019 +18

848 +6

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

3,077 +1

695 +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.

234 +0

5,912 +8

616 +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

1,310 +0

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.

130 -1

5,817 +5

601 +1

nextflow by nextflow-io

A DSL for data-driven computational pipelines

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

86 +0

2,540 +1

590 +2

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

1,167 +4

579 +1

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

1,549 +3

570 +1

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 +1

1,453 +10

544 +2

oneliners by stephenturner

Useful bash one-liners for bioinformatics.

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

157 +0

1,802 +2

511 +0

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

377 +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

973 -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.

112 -1

958 +1

349 +1

seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

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

62 +0

1,312 +2

307 +1

ChIP-seq-analysis by crazyhottommy

ChIP-seq analysis notes from Ming Tang

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

65 +0

708 +6

290 +2

RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

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

78 +0

839 +4

290 +0

bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

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

58 +0

898 +0

283 +1

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

749 -1

270 +1

freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

created at Oct. 13, 2010, 9:34 p.m.

46 +0

746 +2

259 +0