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.

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



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
   Default 1. Samples with total count less than this are deleted.

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

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

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

  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.