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 https://github.com/nextstrain/seasonal-flu/blob/master/config/clades_h1n1pdm_ha.tsv
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 23.1.1 documentation