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

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

msprime

Simulate ARGs and genomic sequence data using population genetic models

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

galaxy-util

Data intensive science for everyone.

hail

Cloud-native genomic dataframes and batch computing

galaxy-tool-util

Data intensive science for everyone.

galaxy-tool-util-models

Data intensive science for everyone.

gget

🧬 gget enables efficient querying of genomic reference databases

bioframe

Genomic interval operations on Pandas DataFrames

biomcp-python

BioMCP: Biomedical Model Context Protocol

goatools

Python library to handle Gene Ontology (GO) terms

ga4gh-vrs

GA4GH Variation Representation Python Implementation

cogent3

Comparative Genomics Toolkit 3

pycirclize

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

cooler

A cool place to store your Hi-C

aegea

Amazon Web Services Operator Interface