OTU accuracy methods
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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 accuracy methods

See also
OTU accuracy results
  Data, commands and scripts
  OTU classification

I used two mock communities (Even and Staggered) of one set of 21 microbial strains created by Haas et al., who created a reference database of 16S sequences in the strains. Reads for these communities were obtained from HMP validation data (454 Titanium) and from a recent paper by Bokulich et al., 2013 (Illumina MiSeq).