I have a question regarding pre.cluster. When this command finds rare sequences that are very similar to abundant sequences, does it (1) remove (i.e. delete) these rare sequences totally, or (2) combine them into the abundant group ?
If the answer is (2), then why would the total number of sequences drop after performing this command? :?
Many thanks for your answer!

#2 - the total number of sequences won’t drop, but the number of unique sequences will drop.

The unique seqs No. will drop.
I think the most important parameter here is the opotion of “diffs”, if the length of your 16S is 300 bp, and you set diffs=1, and calculated the OTUs at 97% sequence identity, then the OTU No. will not drop, will be the same as for no pre.cluster treatment. Any one agree with me?

We recommend diffs=1 for every 100 bp in length.