Analysis of genotyping-by-sequencing (Gbs) data

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TypeBook Chapter
Book titlePlant Bioinformatics
Series titleMethods in Molecular Biology; no. 1374
SubjectBowtie; Demultiplexing, Read map ping; GATK; GBS; Genetic variation; Genotyping; Genotyping -by-sequencing; Haplotype; HaplotypeCaller; Imputation; InDels; Minor allele frequency; Next generation sequencing; RAD-seq; Reduced representation sequencing; SAMtools; Single nucleotide polymorphism; Trimmomatic; UnifiedGenotyper
AbstractThe 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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AffiliationAquatic and Crop Resource Development; National Research Council Canada
Peer reviewedYes
NPARC number23000693
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Record identifier2ebe20b9-f190-4f15-a0a5-a8789df676f1
Record created2016-08-24
Record modified2016-10-27
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