Trevor Bedford

The link to https://www.gisaid.org/help/publish-with-gisaid-references/ now gives a 404. If there is a way to deep-link to specific EPI ISLs it would be useful. I'll leave this issue open and we...

I like the 1+2 proposal above. Keep in mind that even if we could reliably root on "best" (essentially maximizing root-to-tip correlation) we'd be left with an issue of calling...

Thanks Angie! We should indeed revisit these mask sites. They are still currently just `13402`, `24389`, `24390`: https://github.com/nextstrain/ncov/blob/master/defaults/parameters.yaml#L75. The De Maio collection is worth investigating. However, there is increasing evidence...

Collapsable filters would be a nice solution here and shouldn't be too difficult. Would pay dividends in a variety of circumstances.

Trial build running on GISAID data at https://github.com/nextstrain/ncov/actions/runs/2168780200. This will deploy to: - https://nextstrain.org/staging/ncov/gisaid/trial/nextclade-pango/global - https://nextstrain.org/staging/ncov/gisaid/trial/nextclade-pango/africa etc... Trial build running on GenBank data at https://github.com/nextstrain/ncov/actions/runs/2168781757. This will deploy to: -...

I've now done a number of anecdotal comparisons here between `pango_lineage` call from GISAID, which should be latest pangoLEARN and `Nextclade_pango`. From anecdotal investigation, this honestly feels like a wash....

Thinking slightly more broadly, making "correct" calls here (by either pangoLEARN or Nextclade) should mostly be about somehow calling a sequence correctly despite the sequence being shoddy. If I look...

Hmm... but the older pangoLEARN calls by GenBank are clearly an issue relative to Nextclade calls. For example, take a look at: ...

I do think we could eventually aim to have `--method lsd` and `--method treetime` as options to `augur refine`. Or to have other recommended flags to speed up TreeTime.

What happens when viruses with 20 `s1_mutations` exist? Does the ordinal legend end up as 0, 1, ..., 19, 20 (with 21 entries)? I originally didn't have this an ordinal...