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NCBI host fixes needed #141

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jameshadfield opened this issue Feb 25, 2025 · 1 comment
Open

NCBI host fixes needed #141

jameshadfield opened this issue Feb 25, 2025 · 1 comment
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@jameshadfield
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jameshadfield commented Feb 25, 2025

On the latest https://nextstrain.org/avian-flu/h5n1-d1.1/genome tree (~200 new sequences cf. yesterday!)

Image

And in the cattle-outbreak (B3.13) tree, which uses the same NCBI sources:

Image
@jameshadfield jameshadfield added the bug Something isn't working label Feb 25, 2025
@joverlee521 joverlee521 self-assigned this Feb 26, 2025
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Updated host map for everything except "PET FOOD" in #144

Copying comment from #144 (comment)

Note that I did not include "PET FOOD" in this change because I'm unsure how we want to label them.
Previously I added annotations for individual strains that I could track down, but it's not clear what are the latest "PET FOOD" sources.

A couple options:

  1. Leave "PET FOOD" as-is and they will remain as the grey coloring
  2. Map "PET FOOD" to "?" so they are excluded in the host coloring
  3. Map "PET FOOD" to "Environment"

With any of these options, we can always override the general host map with specific annotations if we can track down the original source.

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