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OTU QC: sequences on both strands

See also
  Quality control for OTU sequences

If reads are created from both strands of the gene, then you will tend to get duplicated OTUs where one is the reverse-complement of the other.

To check for reads or OTU sequences on both strands, use the orient command with  -tabbedout orient.txt. Any reference database will do for a quick check, though a large reference database is recommended for orienting the reads in a production pipeline. To get the number of sequences on each strand, use the following Linux command:

cut -f2 orient.txt | sort | uniq -c

All your OTUs should be on the same strand. If not, you need to adjust the pipeline to perform orientation before dereplication (the fastx_uniques step). You could also use:

usearch -cluster_fast otus.fa -id 0.97 -strand both \
  -userout user.txt -userfields query+target+qstrand