feat: Explain our QC, clades and alignment better

[anna-parker]

We should at least link somewhere to the nextclade dataset that we use. Even better might be as @emmahodcroft suggested adding an info page where we describe our annotation process in detail.

• Link to the reference more clearly
• Link to the nextclade dataset: Surface more info on preprocessing tools #3301
• describe our QC scores and clade annotation

[emmahodcroft]

Do we have public nextclade datasets available for each pathogen? I can't remember - I guess that would be a 'step 1' for any where we don't (actually put them on Nextclade)

[emmahodcroft]

As another idea (but may be too manual/too much hard work) - At Nextstrain we have this fig for SC2 which I use all the time. It doesn't work ideally, but something like for each pathogen - if we could get it to automatically generated and update - would probably be the most useful thing for a naive user:

https://github.com/nextstrain/ncov-clades-schema

[anna-parker]

Do we have public nextclade datasets available for each pathogen? I can't remember - I guess that would be a 'step 1' for any where we don't (actually put them on Nextclade)

they are all on nextclade - but some are just on branches and not public merged on main

Datasets to merge:

• CCHF: Cornelius cchfv nextstrain/nextclade_data#200 - no clades or qc
• West Nile: West Nile Virus overview nextstrain/nextclade_data#197 - should be ready to merge
• Ebola: Reference-only Ebola Zaire and Sudan nextstrain/nextclade_data#184 - no clades or qc

[emmahodcroft]

Slightly related to this, we may want to prioritze #3194
Pulling in more QC scores so that people have more metrics by which to judge data quality. This was requested specifically by Aine/Andrew in mpox context, but probably applies more broadly.

(But posting this mostly for visibility, we don't have to try and tackle all of this at once)

[j23414]

+1 for documenting and merging the WNV dataset.

In nextstrain/WNV, we've been using the Pathoplexus API to get the draft WNV global lineage calls:

• Ingest: fetch and append pathoplexus global lineage calls nextstrain/WNV#40

but would love to have more documentation on the reference, QC scores, and other nextclade specific parameters for the WNV dataset.