UCHIME and UCHIME2 are algorithms for detecting chimeric sequences. See the
UCHIME and UCHIME2 papers for details. Note that the accuracy results
reported in the original UCHIME paper are highly over-optimistic due to
unrelaistic benchmark design. This is explained in the UCHIME2 paper.
Stand-alone UCHIME should not be used
in OTU clustering or denoising pipelines because
the cluster_otus and
unoise3 commands have more effective chimera
filters integrated into the algorithms. You will probably get much higher
error rates, both false positives and false negatives, if you use UCHIME
as a stand-alone filtering step.