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feat: Explain our QC, clades and alignment better #3592
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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) |
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: |
they are all on nextclade - but some are just on branches and not Datasets to merge:
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Slightly related to this, we may want to prioritze #3194 (But posting this mostly for visibility, we don't have to try and tackle all of this at once) |
+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: but would love to have more documentation on the reference, QC scores, and other nextclade specific parameters for the WNV dataset. |
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.
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