I would recommend going through the different GWAS tutorials in this page. If you have time for only one tutorial then do the PySeer K-mer association with mixed effects model tutorial. The data can be downloaded from here. Explanation for the different files is available as a table at the start of the GWAS tutorialspage.
N.B. This command may not work python scripts/qq_plot.py penicillin_kmers.txt. Skip it and continue with the rest
ClonalFrameML tutorial. the data for this tutorial should be downloaded from here. Just do the standard model example. This ClonalFrameML command may take 12 hours to run, I would recommend doing that overnight after business hours.