Saccharomyces pastorianus is an allopolyploid sterile yeast hybrid used in brewing to produce lager-style beers. The development of new yeast strains with valuable industrial traits such as improved maltose utilization or balanced flavour profiles are now a major ambition and challenge in craft brewing and distilling industries. Genome-scale computational approaches are opening opportunities to model and predict favourable combination of traits for strain development. However, mining the genome of these complex hybrids is not currently an easy task, due to the high level of redundancy and presence of homologous. Moreover, no genome annotation for these industrial strains have been published. Here, we developed HybridMine, a new user-friendly, open-source tool for functional annotation of hybrid aneuploid genomes of any species by predicting parental alleles including paralogs. As proof of principle, we carried out a comprehensive structural and functional annotation of complex yeast hybrids to enable system biology prediction studies. HybridMine is developed in Python, Perl and Bash programming languages and is available at https://github.com/Sookie-S/HybridMine. ### Competing Interest Statement The authors have declared no competing interest.
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