Monday - Classes from 9:00 to 17:00

 

Session 1- Introduction to Linux and the command line (Dr. Martin Taylor)

 

-       Installation of required software

 

-       Introduction to linux operating system

 

-       Working on the command line. Basic bash shell commands and navigation.

 

-       Introduction to Perl and Python

 

 

Session 2 - Understanding genomic data formats (Dr. Martin Taylor)

 

 

-       Understanding and working with VCF files using VCF tools

 

-       Data conversion and manipulation using Plink

 

-       Text editors

 

 

 

Tuesday  - Classes from 9:00 to 17:00

 

Session 3- Introduction to genetic analysis in R (Dr. Lewis Spurgin)

 

 

-       Introduction to R

 

-       Reading data into R

 

-       Data manipulation in R

 

-       Introduction to Adegenet and other genetics packages

 

 

Session 4- Genomic diversity estimation (Dr. Lewis Spurgin)  

 

 

-       Estimating heterozygosity and nucleotide diversity

 

-       Hardy Weinberg

 

-       Linkage disequilibrium

 

-       Introduction to ggplot2

 

 

 

Wednesday - Classes from 9:00 to 17:00

 

Session 5- Population structure and differentiation (Dr. Martin Taylor & Dr. Lewis Spurgin) 

 

-       Estimating and understanding FST

 

-       Visualising genetic structure using MDS and PCA

 

-       STRUCTURE and related software

 

-       Estimating migration

 

 

Session 6- Identifying selection within populations (Dr. Lewis Spurgin)

 

 

-       Marker-based genetic diversity

 

-       Introduction to sliding windows

 

-       Tajima’s D and related statistics

 

-       Introduction to GO analyses

 

 

 

Thursday - Classes from 9:00 to 17:00

 

Session 7-Identifying selection among populations (Dr. Lewis Spurgin)

 

 

-       FST outlier analysis

 

-       EigenGWAS

 

 

Session 8-Incorporating landscape and seascape into population genomics (Dr. Martin Taylor)

 

 

-       Seascape / landscape genetics

 

-       Environmental  / genomic correlation

 

 

 

Friday  - Classes from 9:00 to 17:00

 

Session 9-Hybridisation and introgression (Dr. Martin Taylor)

 

 

-       Identifying hybrids and introgression using genotype data

 

 

 

Session 10-Summary data troubleshooting session (Dr Martin Taylor & Dr Lewis Spurgin)  

 

 

-       Time to answer questions on any areas covered during week.

 

      -    Talk to us about your own data