Determining whether a sample is H1N1 or H3N2

Question

[ramiro.barrantes]

I have a very simple question but it's just that I am not familiar with viral bioinformatics. Basically, I have a number of clinical H1N1 and H3N2 flu samples amplicon-sequenced using Illumina (I don't know which is H1N1 and which is H3N2), and I would like to figure out their types based on the reference H1N1 and H3N2 reference genomes that I have. In addition, I would like to put them on a tree.

My main question is, in trying to create a consensus sequence for tree building, I need a reference, but what reference do I use if I don't know if the sample is H1N1 or H3N2?

This is probably a very common thing that people do but I have been looking at options and haven't found something suitable

[GenoMax]

So your data is likely to have one or other with the chance that both would be there? Do the analysis with both references in that case. You can use the nextstrain pipeline: https://docs.nextstrain.org/en/latest/learn/about.html