Monday- Classes from 9:30 to 17:30


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 9:30 to 17:30


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 9:30 to 17:30


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 9:30 to 17:30


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 9:30 to 17:30


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