pybedtools | Python Package Wiki

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

ipython-cluster-helper	Simplify IPython cluster start up and use for multiple schedulers.
pysam	pysam
gffutils	Work with GFF and GTF files in a flexible database framework
cyvcf	A fast Python library for VCF files using Cython for speed.
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
sourmash	tools for comparing DNA sequences with MinHash sketches
manta	A Python SDK for Joyent's Manta service
adam	Adam programming language implemented in python
mosaik	Mosaik is a flexible Smart-Grid co-simulation framework.
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!
cyvcf2	fast vcf parsing with cython + htslib

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

pip install pybedtools==0.8.2