Resource for Genotype-by-Sequencing in Ecology and Evolution workshop
| June 11-12 2019 | Ludovic Dutoit and Alana Alexander |
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 two day workshop is designed to show how to process GBS/RAD data through hands-on analysis using the Stacks software pipeline. It will be opened by a mini-symposium where researchers will share experiences using GBS/RADseq to answer questions in their research.
Day 1 - June 11 2019
| Time | Topic | Location |
|---|---|---|
| 09:00-12:30 | Mini Symposium: Genotyping-by-Sequencing and its applications in ecology and evolution | Seminar Room, Benham Building |
| 12:30-13:15 | Lunch Break | |
| 13:15-13:45 | Participant introduction | Seminar Room, Marples Building |
| 13:45-15:00 | Introduction to the command line, part 1 | Seminar Room, Marples Building |
| 15:00-15:30 | Break | |
| 15:30-17:00 | Introduction to the command line, part 2 | Seminar Room, Marples Building |
| 17:00- | End of day 1 - Social | The captain Cook hotel |
| Day 2 | June 12 2019 | |
| 09:00-10:30 | From raw reads to individual samples | Seminar Room, Marples Building |
| 10:30-11:00 | Break | |
| 11:00-12:30 | SNP calling in the absence of a genome part 1 | Seminar Room, Marples Building |
| 12:30-13:30 | Lunch Break | |
| 13:30-15:00 | SNP calling in the absence of a genome part 2 | Seminar Room, Marples Building |
| 15:00-15:30 | Break | |
| 15:30-17:00 | Filtering your SNPs | Seminar Room, Marples Building |
| 17:00 | End of the workshop |