Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies
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.
Key wordsGenotyping by sequencing SNPs SNPcalling Bioinformatics Genotyping
The author acknowledges funding support from the Australian Research Council (Project LP1f10100200). Support is also acknowledged from the Queensland Cyber Infrastructure Foundation (QCIF) and the Australian Partnership for Advanced Computing (APAC).