John Huddleston

One more sanity check before we switch to this ingest approach would be to cross-check the updated strain names against titer record strain names. It seems likely that strains the...

I just ran into a variant of the issue I mentioned above where H1N1pdm titer data include a reference strain named A/SouthAustralia/59/2023. We have this strain in our fauna metadata...

Thanks for figuring that one out, @joverlee521! I think we will usually want to prioritize records with HA over records without, then records with NA, and then everything else.

I'm a little worried about excluding these types of records algorithmically without any notification to us. Ideally, we want to catch these data issues, alert the data provider so they...

@joverlee521 I think we originally asked for the reference panel file and Sheena made it for us. Then later Sheena modified her script that produces the flat files to pull...

Got it. I can't see the latest files any more (curse OneDrive!), but in the last view I had of those files, they included columns for `reference antigen`, `reference passage`,...

I don't depend on `isolate_id` as a field name anywhere. Since Auspice hardcodes separate fields for GISAID and GenBank accessions (without an awareness of segmented viruses), it makes sense to...

Thanks to hard work by @joverlee521, this issue no longer depends on https://github.com/nextstrain/fauna/issues/165 and instead depends on https://github.com/nextstrain/seasonal-flu/issues/234. Once that seasonal flu repo issue is closed, we can revert the...