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LZ.2.1 [C29642T(Orf10:Q29*)]+T2746C, T3055A, T3142C, T22585C, T25496C, G362A, A22995C( Orf1a:D33N,D930E, S:K478T(rev), Orf3a:I35T)
GISAID query: C29642T,T25496C, G362A
No. of seqs: 2(USA 1(from Ja…
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The list of supported clades, which is written down in `mappings.csv`, was taken from nextclade-data, and contains three Delta clades: 21A, 21I and 21J. The latter two do not map to single pango linea…
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Right now, it seems not possible to include `Unknown` lineages in advanced queries.
This would be very useful to filter out sequences that didn't pass pango QC or are otherwise of questionable qual…
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When looking for new mutations e.g. S:Q498R these are placed in lineages (very helpful!). The last step of choosing the actual sequence(s) with the mutation and comparing this to lineage of choice in …
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For CIDO, we represent the different sub-variants of SARS-CoV-2 that emerge, including the PANGO lineage identification (BA.1, BA.2, etc.). However, PANGO lineage identification gives a set of common …
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Right now, we mention lineage-related issues in `lineage_notes.txt` which is a semi structured tsv file.
It would be less bug prone and easier for machines to parse if we added issue-lineage inform…
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I was wondering if it was possible to save the work we do on collections in case something happens, e.g. compromised password or outage etc.
Once export works, one could also do import.
That may…
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When you identify that a recently designated lineage has been discussed in an issue, but the issues has not been mentioned in `lineage_notes.txt` as the person designating wasn't aware of the issue, i…
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There seems to be a large KP.3.1.1+S:S31F branch, while KP.3.1.1 shall have S:31del.
That branch is driven by Denmark seqs which do not handle S:S31del well. When Querying C12616T, A13121T, C2165…
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### Motivation
@Taepper, @chaoran-chen and I have discussed generalizing the Pango wildcard search feature, as monophyletic clade search is important (non-wildcard searches are [paraphyletic](https…