Genotype Python Packages

pandas-plink

PLINK reader for Python.

allelix

🧬 Open-source genotype analysis toolkit

magenpy

Modeling and Analysis of (Statistical) Genetics data in python

lineage

tools for analyzing and exploring genetic relationships

pypgx

A Python package for pharmacogenomics (PGx) research

atarva

ATaRVa - Analysis of Tandem Repeat Variation

aldy

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

snpmatch

A simple python library to identify the most likely strain from the population

the-real-genotools

GenoTools: Advanced Genotype Data Analysis A robust suite for processing genotype data, offering genotype calling (.idat to PLINK), comprehensive sample/variant QC, and ancestry estimation. Ideal for computational biology and genetics research.

mgatk

Mitochondrial genome analysis toolkit.

gennet-forked

Framework for Interpretable Neural Networks

svtyper

Bayesian genotyper for structural variants

sv2

SV2: Support Vector Structural Variation Genotyper

ideal-genom

package to run a genotype quality control pipeline

ideal-genom-qc

package to run a genotype quality control pipeline

plink-bed-reader

Lightweight and memory efficient reader for PLINK BED files. It supports both SNP-major and individual-major formats. Written in Python.