Hi @gdunne,
You can use the command suggested by @Matteo_Scanu to export your table into biom format for other tools, but if the features in the initial table are ASVs, you will always have ASVs.
Just a quick summary, both ASVs and OTUs can be represented within a feature table produced by qiime2, but these are different way to denoise your sequences. ASVs are obtained after an error correction step, OTUs after a clustering of your sequences using a selected similarity threshold (could be either a de-novo clustering or onto a reference they are still called OTUs and may be bit confusing).
So, you can use your dada2 output sequences to further cluster them by q2-vsearch (as you suggest), so that you obtain OTUs.
The question is if you do really need to work with OTUs. Anything you could do with OTUs you can also do with ASVs, but OTUs are dataset-dependents (if you add more sequences to data resulting OTUs may change), ASVs are dataset independent (if two independent datasets contain the same sequences they should produce the same ASVs *), so I usually work with OTUs if I got a specific need (that is very rarely these days).
- Caveat on ASVs, on dada2 the denoising step depend on a random chosen subset of sequences to asses the errors, hence if the two subset, one for each datasets, will be very different in quality or type of sequences it may happen that the resulting ASVs will show some unexpected differences.
Does this help you in your choice?
Cheers
Luca