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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



otutab_otu_subset command

See also
OTU commands
  OTU table
  Making an OTU table (otutab command)

Extract a subset of OTUs from an OTU table. Input must be in QIIME classic format. The -output option gives a filename for the result.

The -labels option gives the name of a text file containing the OTU identifiers. This is a text file with one OTU identifier per line.


usearch -otutab_otu_subset otutable.txt -labels otu_ids.txt -output subset.txt