FIrst thanks for this wonderful software and for keeping it so relevant.
I am working on pipeline optimization and have a mock with 8 bacteria and 2 fungi.
I get about 1200 OTUs and our error rate is 0.08%. I see this is mainly due to the large number of reads going in (around 100-200k). Most reads are coming from those first 8 or so OTUs.
I saw in your 2013 paper you used 5000 total reads per sample but am worried this may not be enough for complex samples.
Might I use 5000 unique reads per sample instead?
What do you think?