Update included and excluded strains for H5N1

nextstrain / avian-flu

Nextstrain build for avian influenza viruses

http://nextstrain.org/avian-flu

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Update included and excluded strains for H5N1 #29

Closed trvrb closed 4 months ago

trvrb commented 4 months ago

This PR updates the 2y H5N1 and H5NX builds to:

include all strains from within the cattle outbreak clade following GISAID strain names rather than SRA strain names
exclude duplicated strains in GISAID

Updates H5N1 cattle outbreak build to:

also include all strain from within the cattle outbreak clade

trvrb commented 4 months ago

Pushed 2y H5N1 builds to staging at:

https://nextstrain.org/staging/avian-flu/h5n1/ha/2y?c=host
https://nextstrain.org/staging/avian-flu/h5n1/pb2/2y?c=host
etc...

Looks generally good. Nice to have the complete metadata. There are 191 cattle viruses on staging from the rebuild, while the live site has 209. So we need to investigate the missing 18 viruses, but I'm going to go ahead and push staging live.