Analysis of genotyping-by-sequencing (Gbs) data

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DOIResolve DOI: https://doi.org/10.1007/978-1-4939-3167-5_15
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Name affiliation
  1. National Research Council of Canada. Aquatic and Crop Resource Development
FormatText, Book chapter
Book titlePlant Bioinformatics
Series titleMethods in Molecular Biology; no. 1374
ISSN1064-3745
ISBN978-1-4939-3166-8
978-1-4939-3167-5
Pages269–284
Subjectbowtie; demultiplexing, Read map ping; GATK; GBS; denetic variation; denotyping; denotyping -by-sequencing; haplotype; haplotypecaller; imputation; InDels; minor allele frequency; next generation sequencing; RAD-seq; reduced representation sequencing; SAMtools; single nucleotide polymorphism; trimmomatic; unifiedgenotyper
Abstract
The development of genotyping-by-sequencing (GBS) to rapidly detect nucleotide variation at the whole genome level, in many individuals simultaneously, has provided a transformative genetic profiling technique. GBS can be carried out in species with or without reference genome sequences yields huge amounts of potentially informative data. One limitation with the approach is the paucity of tools to transform the raw data into a format that can be easily interrogated at the genetic level. In this chapter we describe bioinformatics tools developed to address this shortfall together with experimental design considerations to fully leverage the power of GBS for genetic analysis.
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PublisherSpringer
Springer
LanguageEnglish
Peer reviewedYes
NPARC number23000693
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Record created2016-08-24
Record modified2020-06-18
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