otutab_trim command
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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.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 

USEARCH v11

otutab_trim command

See also
  Making an OTU table (otutab command)
  Setting an OTU abundance cutoff using an octave plot

Remove low-abundance counts, samples and OTUs from an OTU table. The input file must be in QIIME classic format. The output file is specified by the -output option. It is written in QIIME classic format.

Options to set minimum abundances are min_sample_size, min_count, min_freq, min_otu_size and min_otu_freq. See below for definitions and defaults..

Determining an OTU abundance cutoff
See setting an OTU abundance cutoff using an octave plot.

Deleting samples with too few reads
Setting a minimum number of reads for a sample can be quite subjective and depends on the objectives of your analysis. As a rule of thumb, I prefer to have at least 5,000 reads per sample. Example command line:

usearch -otutab_trim otutable.txt -min_sample_size 5000 -output trimmed.txt

Options which specify minimum abundances
-min_sample_size.
   Default 1. Samples with total count less than this are deleted.

-min_count
  Default 1. Minimum count. Counts less than this are set to zero.

-min_freq
  Default 0.0. Minimum frequency, defined as count divided by total sample size. Counts smaller than this are set to zero.

-min_otu_size
  Default 1. Minimum total size for an OTU. OTUs smaller than this are deleted.

-min_otu_freq
  Default 0.0. Minimum size for an OTU as a fraction of all OTUs. OTUs smaller than this are deleted.

If no minimums are specified, the effect is to delete samples and OTUs which have zero.total size.