Create preprocessing vignette

[zenalapp]

To explain how to go from raw whole-genome sequencing data to the files needed for input into regentrans (recombination-filtered variant alignment and phylogeny).

I think this is the best tool to direct them to:
https://github.com/tseemann/snippy

• We outline exactly what commands they need to run.
• And provide a toy example.
• And very clear documentation on what the inputs etc. should be.
• Still need to figure out the best way to tell people to run it if they don't have access to a cluster. Or maybe they do have one they can use?
• Arianna also suggested creating the SNV distance matrix using this on the cluster since it can be computationally intensive to do locally in R: https://github.com/tseemann/snp-dists (should also update the intro vignette to include this as an option)
• Maybe find cloud option?
• Also mention at beginning that should split by MLST (maybe ARIBA or look into other options - Evan might know of others)