pysam | Python Package Wiki

Based on how often these packages appear together in public requirements.txt files on GitHub.

pybedtools	Wrapper around BEDTools for bioinformatics work
biopython	Freely available tools for computational molecular biology.
cyvcf2	fast vcf parsing with cython + htslib
perl	Perl as a Python package
ipython-cluster-helper	Simplify IPython cluster start up and use for multiple schedulers.
ncbi-genome-download	Download genome files from the NCBI FTP server.
ngsutils	NGSUtils - Various utilities for working with NGS data
metaseq	Integrative analysis of high-thoughput sequencing data
manta	A Python SDK for Joyent's Manta service
sourmash	tools for comparing DNA sequences with MinHash sketches
mosaik	Mosaik is a flexible Smart-Grid co-simulation framework.
adam	Adam programming language implemented in python
svtools	Tools for processing and analyzing structural variants
svtyper	Bayesian genotyper for structural variants
beagle	Command line client for Hound
smashbenchmarking	Check the accuracy of one VCF callset against another
canvas	canvas is a simple interface to most common matplotlib functions
pysamstats	A Python utility for calculating statistics against genome position based on sequence alignments from a SAM, BAM or CRAM file.
shapeit	It's Shapely with projections and some other conveniences!

Proportion of downloaded versions in the last 3 months (only versions over 1%).

pip install pysam==0.17.0