mergesam by DarwinAwardWinner

Automate common sam & bam conversions

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

3 +0

6 +0

1 +0

smof by incertae-sedis

Explore and analyze biological sequence data

created at April 27, 2014, 12:34 p.m.

3 +0

15 +0

2 +0

easy_qsub by shenwei356

Easily submitting multiple PBS jobs or running local jobs in parallel. Multiple input files supported.

created at March 9, 2015, 9:40 a.m.

3 +0

28 +0

8 +0

ggd-cli by gogetdata

The command-line interface to GGD

created at April 22, 2016, 3:36 p.m.

5 +0

42 +0

3 +0

squiggle by IQTLabs

📈 DNA Sequence Visualization for Humans

created at July 4, 2018, 3:47 a.m.

6 +0

38 +0

8 +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

wormtable by wormtable

Write-once-read-many table for large datasets.

created at Oct. 27, 2012, 5:01 p.m.

6 +0

27 +0

5 +0

fastqp by mdshw5

Simple FASTQ quality assessment using Python

created at Sept. 23, 2013, 8:01 p.m.

6 +0

107 +0

14 +0

poapy by ljdursi

A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes

created at April 28, 2015, 9:38 p.m.

8 +0

68 +0

12 +0

pyfaidx by mdshw5

Efficient pythonic random access to fasta subsequences

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

9 +0

440 +0

73 +0

bam-toolbox by AndersenLab

A bam toolbox

created at Oct. 28, 2015, 4:36 p.m.

10 +0

1 +0

1 +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

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

gffutils by daler

GFF and GTF file manipulation and interconversion

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

14 +0

267 +2

74 +0

bakta by oschwengers

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

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

14 +0

391 +5

42 +0

redun by insitro

Yet another redundant workflow engine

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

15 +0

486 +2

37 +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

226 +1

83 +0

cruzdb by brentp

python access to UCSC genomes database

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

17 +0

134 +1

41 +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

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