2019-06-11_GBS_EE

Resource for Genotype-by-Sequencing in Ecology and Evolution workshop

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Genotyping-by-Sequencing in Ecology and Evolution:

Practical workshop on the analysis of reduced representation libraries using Stacks

June 11-12 2019 Ludovic Dutoit and Alana Alexander

Description

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.

Schedule

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