Is this tool appropriate to use on non-H5N1 sequences?

[sage-wright]

The paper mainly describes this tool was intended for H5N1. Is this tool appropriate to use on other flu subtypes?

[molly-hetheringtonrauth]

Adding to @sage-wright question: Is this program only intended for H5N1 genomes in the 2.3.4.4 clade?

@sage-wright I tested the tool with H3 and H1 genomes and the program did not assign genotypes. I also tested it with several H5N1 sequences that were not in the 2.3.4.4 clade and the program could not assign genotypes.

[tkanderson]

You can adapt this pipeline through modifying the reference database - currently, this is specific to H5.

For swine IAV, the BV-BRC has swine IAV H1 and H3 HA gene classifications located here: BV-BRC subspecies classification

Our IAV in swine group maintain a swine H1 and H3 WGS classification tool here: octoFLU classification and we have a generic light weight classifier that you can use with your own data and labels here: classLog machine learning classification

For human IAV, nextclade would be useful.

[stuber]

Currently GenoFlu is specific for North American H5N1 genomes in the 2.3.4.4b clade.