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. 2023 Dec 1;39(12):btad691.
doi: 10.1093/bioinformatics/btad691.

ChromaX: a fast and scalable breeding program simulator

Omar G Younis  1 , Matteo Turchetta  1 , Daniel Ariza Suarez  2 , Steven Yates  2 , Bruno Studer  2 , Ioannis N Athanasiadis  3 , Andreas Krause  1 , Joachim M Buhmann  1 , Luca Corinzia  1
Affiliations

ChromaX: a fast and scalable breeding program simulator

Omar G Younis et al. Bioinformatics. .

Abstract

Summary: 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.

Availability and implementation: The documentation is available at https://chromax.readthedocs.io. The code is available at https://github.com/kora-labs/chromax.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
Comparision between the genetic value simulated by ChromaX and AlphaSimR for the same breeding schema. The F0 population contains 50 lines and F1 is created by 200 random biparental crosses. From each line in F1, 100 doubled haploids are obtained and evaluated in head rows (HDRW) using visual selection (low accuracy). Then plants are evaluated with increasing accuracy while reducing the population size. PYT, Preliminary Yield Trial; AYT, Advanced Yield Trial; EYT, Elite Yield Trial
See this image and copyright information in PMC

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