ENH: nextclade extensions to display multiple nomenclatures

[j23414]

Context

To be written

Description

TBD

Examples

Possible solution

• https://github.com/nextstrain/nextclade/blob/master/docs/user/input-files/04-reference-tree.md#extensions

[corneliusroemer]

Do you mean by this to support the new consensus/consortium lineage nomenclature, i.e. https://doi.org/10.1101/2024.05.16.24307504

There are 4 community datasets now for each serotype that annotate the lineages

[j23414]

Originally written, I meant for this issue to allow multiple lineage nomenclature without having to "pick" a correct one. The user could switch between the nomenclature that makes sense for their use-case.

Oh, I definitely support adding rules (to ingest?) to use the 4 community dataset to annotate lineages. I assume the 4 community datasets are DENV1-DENV4 so this would add a single Hill_et_al_2024_nextclade_lineage_calls column to the metadata? Or 4 separate columns?

Feel free to noodle around and add this, I'm a little buried in wnv and lassa pipeline development for a while.

[corneliusroemer]

I don't think I've got time right now to do this - interesting idea to use those datasets to annotate lineages, I was thinking rather to add that lineages system to the Nextstrain nextclade dataset as well from first principles (i.e. not relying on another dataset). The advantage of going from first principles is that you get internal node assignments automatically, rather than having to infer them somehow.