ChromaX is a breeding simulator for large-scale experiments. It is based on JAX and can run smoothly on multiple devices. We designed this library for researchers and breeders with the scope of guiding the design choices of breeding programs.
You can install ChromaX via pip:
pip install chromaxfrom chromax import Simulator
from chromax.sample_data import genetic_map, genome
simulator = Simulator(genetic_map=genetic_map)
f1 = simulator.load_population(genome)
f2, parent_ids = simulator.random_crosses(f1, n_crosses=10, n_offspring=20)@article{10.1093/bioinformatics/btad691,
author = {Younis, Omar G and Turchetta, Matteo and Ariza Suarez, Daniel and Yates, Steven and Studer, Bruno and Athanasiadis, Ioannis N and Krause, Andreas and Buhmann, Joachim M and Corinzia, Luca},
title = "{ChromaX: a fast and scalable breeding program simulator}",
journal = {Bioinformatics},
volume = {39},
number = {12},
pages = {btad691},
year = {2023},
month = {11},
abstract = "{ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two orders of magnitude faster than existing tools with standard hardware. This offers breeders and scientists new opportunities to simulate genetic gain and optimize breeding schemes.The documentation is available at https://chromax.readthedocs.io. The code is available at https://github.com/kora-labs/chromax.}",
issn = {1367-4811},
doi = {10.1093/bioinformatics/btad691},
url = {https://doi.org/10.1093/bioinformatics/btad691},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/39/12/btad691/54143193/btad691.pdf},
}