Hoping to clarify that
DADA2's chimera filtering strategy is a denovo process; that is, there is no use of a set of reference sequence with which to check for chimeras? This older thread from @benjjneb seems to suggest as much.
Fair to say that both DADA2 and Deblur use denovo appproaches for chimera filtering?
I’m curious if users have explored any potential benefit of additional chimera filtering with the vsearch implementation of
uchime_ref? Related: what’s the down side to using a reference library over de novo identification?