Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary

By Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer, Vegard Eldholm. Genome Biology, 2016

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Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/94cf85cec365bfa41c3e9536fa04d8800700c06c