pip install cutadapt==3.5

cyvcf

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

chanjo

Coverage analysis tool for clinical sequencing

bcbio-nextgen

Best-practice pipelines for fully automated high throughput sequencing analysis

pythonpy

python -c, with tab completion and shorthand

gffutils

Work with GFF and GTF files in a flexible database framework

fadapa

FAstqc DAta PArser - A minimal parser to parse FastQC output data in Python

ipython-cluster-helper

Simplify IPython cluster start up and use for multiple schedulers.

bcbreport

report templates for bcbio analysis.

arvados-python-client

Arvados client library

bioblend

CloudMan and Galaxy API library

pybedtools

Wrapper around BEDTools for bioinformatics work

Logbook

A logging replacement for Python

cyvcf2

fast vcf parsing with cython + htslib

canvas

canvas is a simple interface to most common matplotlib functions

smashbenchmarking

Check the accuracy of one VCF callset against another

svtyper

Bayesian genotyper for structural variants

metaseq

Integrative analysis of high-thoughput sequencing data

beagle

Command line client for Hound

svtools

Tools for processing and analyzing structural variants

3.4

36.17%

3.5

12.84%

1.18

8.41%

3.0

3.60%

2.10

2.48%

1.17

2.06%

2.3

1.84%

2.5

1.71%

3.3

1.65%

1.14

1.60%

3.1

1.53%

1.16

1.52%

1.15

1.50%

2.4

1.48%

1.9.1

1.48%

1.17.dev1

1.47%

3.2

1.46%

2.6

1.42%

2.8

1.23%

2.7

1.15%

2.9

1.15%

2.1

1.10%

2.2

1.06%

2.0

1.04%

3.0a2

1.03%