USEARCH manual

Pooling samples for de novo chimera detection

Please note: I now consider de novo UCHIME obsolete for OTU clustering pipelines because UPARSE is a superior approach..

I recommend that you combine samples for de novo chimera detection. (Previously, I have recommended that PCR runs should be processed separately, but I now realize that it is probably better to combine runs). The reasoning is as follows: the main concern is false negatives (FNs), because undetected chimeras are usually more harmful in a biological analysis than false positives (FPs). FNs occur if a chimera has has read abundance that is greater than or equal one of its parents. Combining runs is likely to increase the abundance of a parent (because the same species occurs in multiple samples), but is unlikely to increase the abundance of a chimera. If the chimera is reproduced in a second sample, the parents must also be present and are likely to be present in higher abundances. So pooling should tend to reduce FNs, and there is no reason I can think of why FPs would tend to increase.