Genomics Python Packages

biopython

Official git repository for Biopython (originally converted from CVS)

pyfaidx

Efficient pythonic random access to fasta subsequences

ga4gh-cat-vrs

GA4GH Categorical Variation Representation Python Implementation

ga4gh-va-spec

GA4GH Variation Annotation Python Implementation

ga4gh-vrs

GA4GH Variation Representation Python Implementation

cyvcf2

cython + htslib == fast VCF and BCF processing

mudata

Multimodal Data (.h5mu) implementation for Python

ga4gh

A reference implementation of the GA4GH API

tskit

Population-scale Ancestral Recombination Graph (ARG) library

hail

Cloud-native genomic dataframes and batch computing

bioutils

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

galaxy-tool-util

Data intensive science for everyone.

galaxy-util

Data intensive science for everyone.

msprime

Simulate ARGs and genomic sequence data using population genetic models

biocommons-seqrepo

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

galaxy-tool-util-models

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/).

pyranges

Performant Pythonic GenomicRanges

eutils

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

goatools

Python library to handle Gene Ontology (GO) terms

gget

🧬 gget enables efficient querying of genomic reference databases

biomcp-python

BioMCP: Biomedical Model Context Protocol

bioframe

Genomic interval operations on Pandas DataFrames

cogent3

Comparative Genomics Toolkit 3