Genomics Python Packages

biopython

Official git repository for Biopython (originally converted from CVS)

pyfaidx

Efficient pythonic random access to fasta subsequences

cyvcf2

cython + htslib == fast VCF and BCF processing

mudata

Multimodal Data (.h5mu) implementation for Python

tskit

Population-scale Ancestral Recombination Graph (ARG) library

msprime

Simulate ARGs and genomic sequence data using population genetic models

pyranges

Performant Pythonic GenomicRanges

bioutils

provides common tools and lookup tables used primarily by the hgvs and uta packages

biocommons-seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

galaxy-util

Data intensive science for everyone.

galaxy-tool-util

Data intensive science for everyone.

hgvs

Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

fwdpy11

Forward-time simulation in Python using fwdpp

bioframe

Genomic interval operations on Pandas DataFrames

galaxy-tool-util-models

Data intensive science for everyone.

eutils

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

hail

Cloud-native genomic dataframes and batch computing

gget

🧬 gget enables efficient querying of genomic reference databases

deeptools

Tools to process and analyze deep sequencing data.

pyfamsa

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.

goatools

Python library to handle Gene Ontology (GO) terms

enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

pygenomeviz

A genome visualization python package for comparative genomics

biomcp-python

BioMCP: Biomedical Model Context Protocol