I recently used denoising with dada2 for chimera removal and OTU picking, however I don’t think there is an option for a Silva OTU reference file, which I would like to use. Is there an option for this in dada2 or would I need to use uchime-ref: Reference-based chimera filtering with vsearch (I see there is an option for a reference seq file)?
Dada2 doesn’t do OTU picking, instead it is a denoiser which works in a fundamentally different way than OTU picking methods such as vsearch. As so, doesn’t require a reference file and has its own chimera removal methods so that you don’t need to do additional ones once you have run dada2. If you still need to do OTU picking for some reason (i.e. compare to previous datasets or benchmarking a method) you can feed your denoised feature table to vsearch which can take in a reference database of your choice.
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