Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies

    Research output: Chapter in Book/Conference paperChapter

    1 Citation (Scopus)

    Abstract

    Genotyping by sequencing (GBS) is an emerging technology to rapidly call an abundance of Single Nucleotide Polymorphisms (SNPs) using genome sequencing technology. Several different methodologies and approaches have recently been established, most of these relying on a specific preparation of data. Here we describe our GBS-pipeline, which uses high coverage reads from two parents and low coverage reads from their double haploid offspring to call SNPs on a large scale. The upside of this approach is the high resolution and scalability of the method.

    Original languageEnglish
    Title of host publicationPlant Bioinformatics
    Subtitle of host publicationMethods and Protocols
    EditorsDavid Edwards
    Place of PublicationNew York
    PublisherHumana Press
    Pages285-292
    Number of pages8
    Volume1374
    Edition2nd
    ISBN (Electronic)9781493931675
    ISBN (Print)9781493931668
    DOIs
    Publication statusPublished - 2016

    Publication series

    NameMethods in Molecular Biology
    PublisherSpringer International Publishing
    ISSN (Print)1064-3745

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