Ideas for expanding materials

[tavareshugo]

Several loose comments in the thread below. I'll keep editing this top comment to keep track of ideas.

• Create an appendix of common species (e.g. based on participants in the course) and what workflows would be suitable for them.
• Related to the previous point, could include some worked examples of non-human bacterial (e.g. animal or plant pathogens) - this could be added as appendix
• Lineage assignment and clustering with fastBAPS (see comment below)
• ML applications
• Mutational spectra - possibly separate half-day module
• GWAS practical - possibly should be a separate half-day module
• Phage/Plasmid assembly (challenging topic, usually requires long read data; could have a talk in the future if we find a speaker, or perhaps its own separate module)
• GWAS lecture
• Timed trees: introduce the concept and how they can be estimated. Could introduce both ML and Bayesian methods. As a practical could just use treetime.
• Typing schemes: introduce MLST, cgMLST, pros and cons.
• Visualisation: additional and/or more advanced phylogeny visualisations using ggtree (but this adds an extra hard prerequisite)

[tavareshugo]

• Lineage assignment and clustering: a larger dataset (maybe starting from preprocessed FASTA files) where fastBAPS can be run. To cover the workflow of generating an initial tree, cluster with fastBAPS, generate reference-based alignments for each cluster, followed by gubbins and iqtree

[tavareshugo]

• Mutational spectra: include Chris' talk in the schedule (and in the future could consider a practical?)

[tavareshugo]

• GWAS - lecture and/or practical with pyseer