A tutorial/assignment on how to get from raw sequencing reads to a basic population genetic analysis.
This tutorial treats the case of short read based whole genome resequencing with an existing reference genome.
It is logical to start with Alignment and Variant Calling. The variant callset produced in this part is then used in Population Genomics to run some basic population genomic analysis. This tutorial can be run in parallel with the R plotting tutorial that shows how to plot the results.