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nextstrain / avian-flu

Nextstrain build for avian influenza viruses
http://nextstrain.org/avian-flu
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Full genome analysis of h5n1-cattle-outbreak #21

Closed jameshadfield closed 2 months ago

jameshadfield commented 2 months ago

~Main TODO is to join the genbank files & translate~

~Tree available at https://nextstrain.org/staging/avian-flu/h5n1/selected-strains-genome~

jameshadfield commented 2 months ago

@lmoncla @trvrb full genome build is working well and is up at https://nextstrain.org/avian-flu/h5n1-cattle-outbreak/genome

Note that fauna only has ~29 strains of this clade, so you have to use a different data source for this build. It's also a little tricky to run on AWS as it needs input files from the main Snakemake build, but it runs in about 5min on a laptop so I suggest running everything locally for now.

One thing we have to be cognisant of is updating the include strains list as new sequences arrive, which obviously won't scale but we can iterate on this. Perhaps here a hamming-distance include-new-seqs approach would work, but I haven't thought about it much.

trvrb commented 2 months ago

This is working well for me. I like the general strategy here as well. I'm going to go ahead and merge this. Thank you @jameshadfield!