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.
authors.affiliation: School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia. philipp.bayer@uqconnect.edu.au.
authors.forename: Philipp Emanuel
authors.initials: PE
authors.lastname: Bayer
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005785:Gene Conversion; D023281:Genomics / Q000379:methods*; D060005:Genotyping Techniques / Q000379:methods*; D006238:Haploidy; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: Bioinformatics; Genotyping; Genotyping by sequencing; SNP call ing; SNPs