title: 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 .
authors.affiliation: Domain of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway. ola.brynildsrud@fhi.no.
authors.forename: Ola
authors.identifier: 0000-0001-7566-4133
authors.initials: O
authors.lastname: Brynildsrud
authors.affiliation: Domain of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.
authors.forename: Jon
authors.initials: J
authors.lastname: Bohlin
authors.affiliation: Domain of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.|Hanze University of Applied Sciences, Groningen, The Netherlands.
authors.forename: Lonneke
authors.initials: L
authors.lastname: Scheffer
authors.affiliation: Domain of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.
authors.forename: Vegard
authors.initials: V
authors.lastname: Eldholm
keywords: Accessory genome; Annotation; Association; Bacteria; Genome-wide association studies (GWAS); Genomics; Next-generation sequencing (NGS); Pan-genome; Prokaryote; Python; Whole-genome sequencing (WGS)