Population Variation Genetics

To familiarise students with the molecular and analytical aspects of the genetic screening method Genotype-By-Sequencing (GBS).  

GBS involves the use of short-read sequence data produced from Reduced Representation Libraries (RRL), such as Restricted Site Associated DNA (RAD-tags). GBS libraries can provide a dense set of single nucleotide polymorphisms.

SNP markers are spread evenly across a genome. These markers are useful for a variety of genetic and genomic analyses in both model and non-model organisms. Students will gain experience with the computational pipeline 'Stacks' which was designed for the analysis of such data.

The course will focus on the necessary UNIX skills to handle GBS data, as well as how to clean and demultiplex Illumina sequences. Students will then analyse RAD-seq data de novo to perform a population analysis without the aid of a reference genome using Stacks and structure, and from an organism with a reference genome to generate Fst measures and identify signatures of selection.

Course Prerequisites

Those accepted will be in the planning stages, or producing a Genotype-By-Sequencing project.

Target audience

Graduate students, post-docs and PI's.