Roder, Thomas; Pimentel, Grégory; Fuchsmann, Pascal; Stern, Mireille Tena; von Ah, Ueli; Vergères, Guy; Peischl, Stephan; Brynildsrud, Ola; Bruggmann, Rémy; Bär, Cornelia (2024). Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes. Genome biology, 25(1) BioMed Central 10.1186/s13059-024-03233-7
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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.
Item Type: |
Journal Article (Original Article) |
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Division/Institute: |
08 Faculty of Science > Department of Biology > Bioinformatics and Computational Biology |
Graduate School: |
Graduate School for Cellular and Biomedical Sciences (GCB) |
UniBE Contributor: |
Roder, Thomas, Peischl, Stephan, Bruggmann, Rémy |
ISSN: |
1474-760X |
Publisher: |
BioMed Central |
Language: |
English |
Submitter: |
Pubmed Import |
Date Deposited: |
12 Apr 2024 14:57 |
Last Modified: |
12 Apr 2024 15:06 |
Publisher DOI: |
10.1186/s13059-024-03233-7 |
PubMed ID: |
38605417 |
Uncontrolled Keywords: |
BGWA Bacteria Fermented food GWAS Genotype-phenotype association Metabolite Microbial genome-wide association studies Omics Pan-genome Prokaryote |
BORIS DOI: |
10.48350/195911 |
URI: |
https://boris.unibe.ch/id/eprint/195911 |
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