Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2023.07.06.547949v1?rss=1
Authors: Freudenberg, A., Vandenplas, J., Schlather, M., Pook, T., Evans, R., ten Napel, J.
Abstract:
In the last two decades, a number of so-called single-step models have been suggested to incorporate both pedigree and genomic data in statistical breeding value estimation for breeding programs. Yet, steadily growing population sizes and the suboptimal use of computational resources are pushing the practical application of these models to their limits. As an extension to the miraculix package, we have developed tailored solutions for the computation of genotype matrix multiplications, a critical bottleneck when iteratively solving equation systems associated with single-step models. Targeting modern Nvidia(R) GPUs as well as a broad range of CPU architectures, our implementation significantly accelerates the estimation of breeding values in large population sizes. miraculix is a C/CUDA library released under the Apache 2.0 license. It is freely available at https://github.com/alexfreudenberg/miraculix.
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