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Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes.

Institutional Repository Agroscope

Roder T., Pimentel G., Fuchsmann P., Tena Stern M., Von Ah U., Vergères G., Peischl S., Brynildsrud O., Bruggmann R., Bär C.

Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes.

Genome Biology, 25, 2024, 1-19.

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Résumé:

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.

ISSN en ligne: 1474-7596
Digital Object Identifier (DOI): https://doi.org/10.1186/s13059-024-03233-7
ID publication (Code web): 56165 Envoyer par e-mail

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Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes.

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