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

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...

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Autores principales: Brynildsrud, Ola, Bohlin, Jon, Scheffer, Lonneke, Eldholm, Vegard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5124306/
https://www.ncbi.nlm.nih.gov/pubmed/27887642
http://dx.doi.org/10.1186/s13059-016-1108-8
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author Brynildsrud, Ola
Bohlin, Jon
Scheffer, Lonneke
Eldholm, Vegard
author_facet Brynildsrud, Ola
Bohlin, Jon
Scheffer, Lonneke
Eldholm, Vegard
author_sort Brynildsrud, Ola
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-1108-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-51243062016-12-08 Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary Brynildsrud, Ola Bohlin, Jon Scheffer, Lonneke Eldholm, Vegard Genome Biol Software 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-1108-8) contains supplementary material, which is available to authorized users. BioMed Central 2016-11-25 /pmc/articles/PMC5124306/ /pubmed/27887642 http://dx.doi.org/10.1186/s13059-016-1108-8 Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Brynildsrud, Ola
Bohlin, Jon
Scheffer, Lonneke
Eldholm, Vegard
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
title Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
title_full Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
title_fullStr Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
title_full_unstemmed Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
title_short Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
title_sort rapid scoring of genes in microbial pan-genome-wide association studies with scoary
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5124306/
https://www.ncbi.nlm.nih.gov/pubmed/27887642
http://dx.doi.org/10.1186/s13059-016-1108-8
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