-uparseout option
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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.



-uparseout option

Output file, UPARSE tabbed format. Supported by cluster_otus and uparse_ref. There are five or six fields, as shown in the following table.

Field   Description
1   Query label.
2   Classification.

For cluster_otus, this field is otu, match or chimera.
  otu: New OTU. Sequence is <97% to existing OTU and is not chimeric.
  match: Assigned to existing OTU (>= 97% match).
  chimera: Sequence is chimeric.

For uparse_ref, it is perfect, good, noisy, chimera or other.
  perfect: 100% match to a reference sequence.
  good: >=99% match to reference sequence.
  noisy: >= 97% match to reference sequence
  chimera: matches chimeric model constructed from reference sequences
  other: < 97% match and not chimeric.

3   Percent identity between the query sequence and the top hit in the reference database. With cluster_otus, the reference database is the current set of OTUs. If no hit was found, this field is set to *,
4   Percent identity between the query sequence and the maximum parsimony model. If no model is made, e.g. because the database is empty, then this field is set to *.
5   OTU label(s). If the model is chimeric, then the labels and start-end segment coordinates are given. Otherwise, the label of the reference sequence. For cluster_otus, this will be the label of an existing OTU. If no model is constructed, this field is set to *.

Example output

Even1.7;size=4383;   otu      *     *       OTU_1
Even1.145;size=21;   otu      *     *       OTU_2
Even1.1733;size=20;  match    99.5  *       OTU_2
Even1.942;size=20;   chimera  94.0  100.0   OTU_1(1-141)+OTU_2(142-200)
Even1.1821;size=20;  match    98.5  *       OTU_1
Even1.1415;size=19;  match    97.0  *       OTU_2