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

226 +0

83 +0

cyvcf by arq5x

A fast Python library for VCF files leveraging Cython for speed.

created at April 12, 2012, 6:51 p.m.

6 +0

52 +0

13 +0

PyVCF by jamescasbon

A Variant Call Format reader for Python.

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

31 +0

393 +1

199 +0

gffutils by daler

GFF and GTF file manipulation and interconversion

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

14 +0

267 +0

74 +0

cruzdb by brentp

python access to UCSC genomes database

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

17 +0

134 +0

42 +1

mergesam by DarwinAwardWinner

Automate common sam & bam conversions

created at Aug. 26, 2011, 2:19 p.m.

3 +0

6 +0

1 +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

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

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 +0

104 +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