genomicSimulation: fast R functions for stochastic simulation of breeding programs

Abstract

Simulation tools are key to designing and optimising breeding programs that are many-year, high-effort endeavours. Tools that operate on real genotypes and integrate easily with other analysis software are needed for users to integrate simulated data into their analysis and decision-making processes. This paper presents genomicSimulation, a fast and flexible tool for the stochastic simulation of crossing and selection on real genotypes. It is fully written in C for high execution speeds, has minimal dependencies, and is available as an R package for integration with R’s broad range of analysis and visualisation tools. Comparisons of a simulated recreation of a breeding program to the real data shows that the tool’s simulated offspring correctly show key population features. Both versions of genomicSimulation are freely available on GitHub: The R package version at https://github.com/vllrs/genomicSimulation/ and the C library version at https://github.com/vllrs/genomicSimulationC