1. Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes
- Author
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Thomas Roder, Grégory Pimentel, Pascal Fuchsmann, Mireille Tena Stern, Ueli von Ah, Guy Vergères, Stephan Peischl, Ola Brynildsrud, Rémy Bruggmann, and Cornelia Bär
- Subjects
Prokaryote ,Bacteria ,Pan-genome ,Metabolite ,Microbial genome-wide association studies ,GWAS ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving 40–60% of bacterial genes undescribed. To address this bottleneck, we introduce Scoary2, an ultra-fast microbial genome-wide association studies (mGWAS) software. With its data exploration app and improved performance, Scoary2 is the first tool to enable the study of large phenotypic datasets using mGWAS. As proof of concept, we explore the metabolome of yogurts, each produced with a different Propionibacterium reichii strain and discover two genes affecting carnitine metabolism.
- Published
- 2024
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