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ktmeaton / ncov-recombinant

Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
MIT License
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Use nextclade dataset Auspice tree for lineage hierarchy #185

Closed ktmeaton closed 1 year ago

ktmeaton commented 1 year ago

The lineages yaml is not updated as fast as nextclade is.

The nextclade Auspice JSON is updated more frequently.

ktmeaton commented 1 year ago

I'm going to supplement the nextclade tree by adding in the latest lineages from https://github.com/cov-lineages/pango-designation/blob/master/lineage_notes.txt.

ktmeaton commented 1 year ago

Instead, I'm creating a "bleeding-edge" phylogeny of the latest designations from pango using the pango_aliasor library.