See also
Quality control
for OTU sequences
Cross-talk is a common problem in next-generation amplicon sequencing where multiplexed reads are assigned to the wrong sample. For more details and discussion, see UNCROSS paper.
The uncross command can be used to check for
cross-talk, but this is very difficult unless you have a
mock community control sample. Even then,
reliable detection is only possible for reads which are misassigned to the
mock samples, you can't see cross-talk between the "real" samples in most
cases. The annot command is also useful for
identifying unexpected mock OTUs as cross-talk or contaminants.
If you do have a mock control sample (good for you!), then the best way to
check for cross-talk is to get the OTU sequences which have one or more
reads assigned to the mock samples. Align these OTUs to the known reference
sequences in the mock community. If you don't have reference sequences, let
me know -- I have high-quality databases for several popular mock
communities and will be glad to post them for you.