Unclear where VP1 and WGS clade information is from.

[m-d-grunnill]

Dear @emmahodcroft

It is unclear to me where the information information in the following files is from:

• genome/config/clades.tsv
• vp1/config/clades.tsv

I suspect these are downloaded and decompressed in the subsection Setup > Quickstart.
Is this the case?

[emmahodcroft]

Hi @m-d-grunnill,
Sorry, I'm not sure I fully understand the question. These should just be part of the enterovirus_d68 repository: here for genome and here for VP1.

The clade definitions themselves are based on previous assignments of clades based on EV-D68 papers and assignments on Genbank - however since these aren't fully defined in a phylogenetic sense (list of full mutations) I have assigned them by mutations to the tree (as is necessary in augur).

I'm afraid the EV-D68 repository doesn't have any kind of Quickstart set up or similar - one simply clones the repository and uses this is the run directory. The steps to download from Genbank will download sequences, but that's all (no additional code). I hope this helps!