Genotype by Sequencing

With the age of high-throughput sequencing, several techniques have been developed to genotype thousands of markers across hundreds of individuals at relatively low-cost. One group of those methods, Genotyping-by-Sequencing (GBS) cuts down on the amount of the genome sequenced by using restriction enzymes to repeatedly sequence the same genomic locations across individuals. The thousands of loci sequenced can bring high resolution to population genomic or phylogenomic analyses at a fraction of the cost associated with whole genome sequencing.

This one day workshop is designed to show how to process GBS/RAD data through hands-on analysis using the Stacks software pipeline.

Prerequisites

All pre-requisites are taken care of if you are using this lesson at the Otago Bioinformatics Spring School 2021.

Please see the setup instructions if you wish to undertake this workshop on your own computer.

Schedule

	Setup	Download files required for the lesson
00:00	1. Data101: From raw data to individual samples files	How do we process data from raw reads to individual fastq files?
00:00	2. De-novo assembly without a reference genome	How can we identify genetic variants without a reference genome? How to optimise parameters in the Stacks parameter space? How to access the full extent of the cluster resources?
00:00	3. Assembly with a reference genome	How do we identify genetic variants if we have a reference genome?
00:00	4. Population genetics analyses	How do I navigate filtering my SNPs? How can I quickly visualise my data?
00:00	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.