Reduced representation genome sequencing (RADseq) data analysis for population genetics, association studies and phylogenetics
DATES 4-8 December 2017
INSTRUCTORS Dr. Naiara Rodriguez-Ezpeleta (Senior Researcher, Marine Research Division, AZTI, Spain) https://www.physalia-courses.org/instructors/t19/
Dr. Josephine Paris (University of Exeter, UK) https://www.physalia-courses.org/instructors/t21/
Reduced representation genome sequencing methods are revolutionizing evolutionary analyses of non-model organisms. Several data generation and data analysis protocols have been developed to generate thousands of sequence variants in hundreds of individuals at relative low cost and speed. In this course, we will introduce the different approaches for obtaining reduced representation genome sequencing data and will specially focus on the data analysis. We will cover all necessary steps to obtain genome variants from short read data that are informative for population genetics, phylogenetic and association studies.
The workshop will be delivered over the course of five days. Each day will include an introductory lecture with class discussion of key concepts. The remainder of each day will consist of practical hands-on sessions. These sessions will involve a combination of both mirroring exercises with the instructor to demonstrate a skill as well as applying these skills on your own to complete individual exercises. After and during each exercise, interpretation of results will be discussed as a group.
WHO SHOULD ATTEND
This workshop is aimed at researchers and technical workers who are generating and/or analyzing reduced representation genome sequencing data (RAD-seq, ddRAD, 2bRAD, GBS,…). Examples demonstrated in this course will involve primarily non-model organisms and examples of applications of this data type for different purposes will be covered.
Attendees should have a background in biology. We will dedicate one session to some basic and advanced Linux concepts. Attendees should have also some familiarity with genomic data such as that arising from NGS sequencers.
Monday 4th – Classes from 09:30 to 17:30
Lecture 1 – Introduction to high-throughput reduced representation data
Lab 1 – Computer environment set up and introduction to UNIX
Lab 2 – High-throughput data quality assessment
Tuesday 5th – Classes from 09:30 to 17:30
Lecture 2 – Overview of reduced representation library sequencing data analysis strategies: considerations depending of each case study
Lab 3 – Data preprocessing
Wednesday 6th – Classes from 09:30 to 17:30
Lecture 3 – De novo and reference based loci assembly and informative marker selection
Lab 4 – De novo loci assembly
Lab 5 – Reference genome based loci assembly
Thursday 7th – Classes from 09:30 to 17:30
Lecture 4 – Applications of reduced representation sequencing data to population genetics, genome wide association studies and phylogenetics
Lab 6 – From assembled loci to informative marker selection
Friday 8th – Classes from 09:30 to 17:30
Lecture 5 - Review. Questions and Answers. Open discussion.
Lab 7 – Continue previous unfinished exercises or work on your own data
The cost is 480 euros (VAT included) including course material and refreshments. We also offer an all-inclusive package at 745 euros (VAT included), which includes course material, refreshments, accommodation and meals.