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

5,808 +7

600 -1

biopython by biopython

Official git repository for Biopython (originally converted from CVS)

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

171 +0

4,148 +17

1,709 +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.

160 +0

3,070 +9

695 -3

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

hail by hail-is

Cloud-native genomic dataframes and batch computing

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

55 +0

934 +3

236 +0

RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

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

78 +0

834 +7

289 +0

ChIP-seq-analysis by crazyhottommy

ChIP-seq analysis notes from Ming Tang

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

65 +0

699 +1

288 +1

redun by insitro

Yet another redundant workflow engine

created at Nov. 4, 2021, 12:14 a.m.

15 +0

483 +2

36 +0

pyfaidx by mdshw5

Efficient pythonic random access to fasta subsequences

created at Sept. 12, 2013, 7:02 p.m.

9 +0

438 +0

72 +0

PyVCF by jamescasbon

A Variant Call Format reader for Python.

created at Oct. 30, 2011, 4:52 p.m.

31 +0

392 +1

198 +0

bakta by oschwengers

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

created at Jan. 15, 2020, 11:08 p.m.

14 +0

385 +2

42 +0

pyensembl by openvax

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

created at April 14, 2014, 3:23 p.m.

22 +0

352 +0

66 +1

pybedtools by daler

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

created at May 14, 2010, 9:09 p.m.

17 +0

293 +2

103 +0

bioservices by cokelaer

Access to Biological Web Services from Python.

created at Aug. 28, 2014, 3:24 p.m.

18 +0

271 +0

61 +0

gffutils by daler

GFF and GTF file manipulation and interconversion

created at Oct. 12, 2011, 1:48 p.m.

14 +0

264 +0

74 +0

bamsurgeon by adamewing

tools for adding mutations to existing .bam files, used for testing mutation callers

created at May 10, 2012, 10:18 p.m.

15 +0

225 +0

83 +1

AfterQC by OpenGene

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

created at Aug. 4, 2015, 2:08 p.m.

20 +0

201 +0

51 +0

ruffus by cgat-developers

CGAT-ruffus is a lightweight python module for running computational pipelines

created at Jan. 6, 2013, 10:20 p.m.

11 +0

171 +0

34 +0

cruzdb by brentp

python access to UCSC genomes database

created at Sept. 2, 2011, 3:36 p.m.

17 +0

133 +0

41 +0

seqmagick by fhcrc

An imagemagick-like frontend to Biopython SeqIO

created at Nov. 24, 2010, 12:48 a.m.

12 +0

108 +0

22 +0