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

Philipp Emanuel Bayer

doi:10.1007/978-1-4939-3167-5_16

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

Philipp Emanuel Bayer

Research output: Chapter in Book/Conference paper › Chapter

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 language	English
Title of host publication	Plant Bioinformatics
Subtitle of host publication	Methods and Protocols
Editors	David Edwards
Place of Publication	New York
Publisher	Humana Press
Pages	285-292
Number of pages	8
Volume	1374
Edition	2nd
ISBN (Electronic)	9781493931675
ISBN (Print)	9781493931668
DOIs	https://doi.org/10.1007/978-1-4939-3167-5_16
Publication status	Published - 2016

Publication series

Name	Methods in Molecular Biology
Publisher	Springer International Publishing
ISSN (Print)	1064-3745

Access to Document

10.1007/978-1-4939-3167-5_16

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

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.",

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

Plant Bioinformatics: Methods and Protocols. ed. / David Edwards. Vol. 1374 2nd. ed. New York : Humana Press, 2016. p. 285-292 (Methods in Molecular Biology).

Research output: Chapter in Book/Conference paper › Chapter

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KW - Computational Biology

KW - Gene Conversion

KW - Genomics

KW - Genotyping Techniques

KW - Haploidy

KW - Polymorphism, Single Nucleotide

KW - Sequence Analysis, DNA

KW - Software

KW - Journal Article

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