Genomics Python Packages

biopython

Official git repository for Biopython (originally converted from CVS)

pyfaidx

Efficient pythonic random access to fasta subsequences

eutils

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

cyvcf2

cython + htslib == fast VCF and BCF processing

mudata

Multimodal Data (.h5mu) implementation for Python

bioutils

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

pyfamsa

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

pyranges

Performant Pythonic GenomicRanges

biocommons-seqrepo

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

mappy

A versatile pairwise aligner for genomic and spliced nucleotide sequences

hgvs

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

gget

🧬 gget enables efficient querying of genomic reference databases

galaxy-util

Data intensive science for everyone.

galaxy-tool-util

Data intensive science for everyone.

marsilea

Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

bioframe

Genomic interval operations on Pandas DataFrames

hail

Cloud-native genomic dataframes and batch computing

galaxy-tool-util-models

Data intensive science for everyone.

tskit

Population-scale Ancestral Recombination Graph (ARG) library

enformer-pytorch

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

msprime

Simulate ARGs and genomic sequence data using population genetic models

biomcp-python

BioMCP: Biomedical Model Context Protocol

pygenomeviz

A genome visualization python package for comparative genomics

goatools

Python library to handle Gene Ontology (GO) terms