Is there any example for handling HIV data?

[Liam]

Dear @ivan-aksamentov,

Could I know if there is any example for handling HIV data to run alignment, mutation calling, clade assignment, quality checks and phylogenetic placement?

[Ivan Aksamentov]

@liamxg There isn't at this time, but we experimented internally a little with it. There is a few problems to solve with regards to HIV, because it's a very diverse virus.

In Nextclade v3 it will be easier to create datasets, so you could create your own (or multiple of them). Here is a preview of how it might look like in Nextclade v3: https://github.com/nextstrain/nextclade_data/blob/master/docs/dataset-curation-guide.md

[Liam]

Dear @ivan-aksamentov,

Thanks. Agree with you that HIV is a very diverse virus. I will look for Nextclade v3 first.