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

ABSTRACT: 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 .

SUBMITTER: Brynildsrud O 

PROVIDER: S-EPMC5124306 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature