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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-12

AUTHORS

Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer, Vegard Eldholm

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 . More... »

PAGES

238

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13059-016-1108-8

DOI

http://dx.doi.org/10.1186/s13059-016-1108-8

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1016471298

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27887642


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