For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
38
views
22
references
 Top references
cited by
194
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      316
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

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

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          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.

          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.

          Related collections

          Most cited references22

          • Record: found
          • Abstract: found
          • Article: not found

          Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".

          H Tettelin, V Masignani, M. J. Cieslewicz … (2005)
          The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.
          Article 0 comments Cited 914 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            The microbial pan-genome.

            Duccio Medini, Claudio Donati, Hervé Tettelin … (2005)
            A decade after the beginning of the genomic era, the question of how genomics can describe a bacterial species has not been fully addressed. Experimental data have shown that in some species new genes are discovered even after sequencing the genomes of several strains. Mathematical modeling predicts that new genes will be discovered even after sequencing hundreds of genomes per species. Therefore, a bacterial species can be described by its pan-genome, which is composed of a "core genome" containing genes present in all strains, and a "dispensable genome" containing genes present in two or more strains and genes unique to single strains. Given that the number of unique genes is vast, the pan-genome of a bacterial species might be orders of magnitude larger than any single genome.
            Article 0 comments Cited 508 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              Adjusted P-Values for Simultaneous Inference

              S. Wright (1992)
              Article 0 comments Cited 199 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Contributors
                Ola Brynildsrud:
                ORCID: http://orcid.org/0000-0001-7566-4133
                ola.brynildsrud@fhi.no
                Jon Bohlin: jon.bohlin@fhi.no
                Lonneke Scheffer: lonsch96@live.nl
                Vegard Eldholm: vegard.eldholm@fhi.no
                Journal
                Journal ID (nlm-ta): Genome Biol
                Journal ID (iso-abbrev): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central (London )
                ISSN (Print): 1474-7596
                ISSN (Electronic): 1474-760X
                Publication date (Electronic): 25 November 2016
                Publication date PMC-release: 25 November 2016
                Publication date Collection: 2016
                Volume: 17
                Electronic Location Identifier: 238
                Affiliations
                [1 ]Domain of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
                [2 ]Hanze University of Applied Sciences, Groningen, The Netherlands
                Author information
                http://orcid.org/0000-0001-7566-4133
                Article
                Publisher ID: 1108
                DOI: 10.1186/s13059-016-1108-8
                PMC ID: 5124306
                PubMed ID: 27887642
                SO-VID: ae48d508-f646-4a27-b953-11758a2b69a1
                Copyright © © The Author(s). 2016
                License:

                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.

                History
                Date received : 20 October 2016
                Date accepted : 11 November 2016
                Categories
                Subject: Software
                Custom metadata
                issue-copyright-statement © The Author(s) 2016

                ScienceOpen disciplines: Genetics
                Keywords: pan-genome,accessory genome,annotation,prokaryote,genomics,whole-genome sequencing (wgs),next-generation sequencing (ngs),python,bacteria,genome-wide association studies (gwas),association
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: pan-genome, accessory genome, annotation, prokaryote, genomics, whole-genome sequencing (wgs), next-generation sequencing (ngs), python, bacteria, genome-wide association studies (gwas), association

                Comments

                Comment on this article

                scite_

                Similar content316

                See all similar

                Cited by259

                See all cited by

                Most referenced authors709

                See all reference authors