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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 results

See also
  OTU benchmark


Species per OTU on HMP mock communities
Since most methods produce many OTUs per species, I used the inverse ratio, i.e. number of species divided by number of OTUs, to produce a measure that usually falls in the range zero to one. I estimated the number of species as the sum of the number of mock species found, plus the number of OTUs classified as Contaminant.

For the 454 datasets, the QIIME species per OTU values are too small to be visible, ranging from 0.005 (Stag2P) to 0.014 (Stag1P).

For the Illumina datasets (not shown in figure), UPARSE OTUs have 0.95 species per OTU, while QIIME has 0.1 species per OTU.

The much closer agreement between the number of OTUs and the number of mock species plus detected contaminants achieved by UPARSE compared to the other assessed pipelines suggests that UPARSE may generate OTUs that are closer to 1:1 correspondence with species on samples collected in vivo.

Edgar, R.C. (2013) UPARSE: Highly accurate OTU sequences from microbial amplicon reads, Nature Methods [Pubmed:23955772dx.doi.org/10.1038/nmeth.2604].