OTU table output files
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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.



OTU table output files

See also
  OTU / denoising pipeline
  Generating an OTU table

Commands which support generating OTU tables understand the following options. The most commonly used commands are otutab and closed_ref.

-mapout filename
    Tab-separated text file which maps reads to OTUs.
    There is one read per line with two fields: the read label and the OTU identifier.

-otutabout filename
    QIIME classic tabbed text format.

-biomout filename
BIOM v1.0 format (JSON). The biom utility can be used to convert to BIOM v2.1 format (HDF5).

-mothur_shared_out filename
    Mothur "shared" file.