This is a Q&A that happened privately that I’m open sourcing for future reuse
I am using NextStrain to assign clades to the H1N1 viruses in my dataset, but I noticed there were many unassigned viruses. For the H1N1 clades prior to 2014 that aren’t assigned by Nextclade, could you share the criteria NextStrain uses to define these pre-2014 clades (e.g., clade 7) so I could apply the same criteria to my data and be consistent with NextStrain?
The clade defining mutations are contained in the
clades.tsv file in the seasonal-flu repo seasonal-flu/clades_h1n1pdm_ha.tsv at master · nextstrain/seasonal-flu · GitHub
If you are making a build using augur tools, you can assign these clades using the
augur clades command using that
clades.tsv from above: augur clades — Augur 17.1.0 documentation