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

Autor: Roder T; Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, CH-3012, Switzerland.; Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012, Bern, Switzerland., Pimentel G; Methods development and analytics, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland., Fuchsmann P; Food microbial systems, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland., Stern MT; Food microbial systems, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland., von Ah U; Food microbial systems, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland., Vergères G; Food microbial systems, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland., Peischl S; Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, CH-3012, Switzerland., Brynildsrud O; Norwegian Institute of Public Health, Oslo and Norwegian University of Life Science, Ås, Norway., Bruggmann R; Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, CH-3012, Switzerland. remy.bruggmann@unibe.ch., Bär C; Methods development and analytics, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2024 Apr 11; Vol. 25 (1), pp. 93. Date of Electronic Publication: 2024 Apr 11.
DOI: 10.1186/s13059-024-03233-7
Abstrakt: 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.
(© 2024. The Author(s).)
Databáze: MEDLINE
Externí odkaz: