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 paperChapterpeer-review

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
Pages405-413
Number of pages9
Edition3
ISBN (Electronic)978-1-0716-2067-0
DOIs
Publication statusPublished - 2022

Publication series

NameMethods in Molecular Biology
Volume2443
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

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