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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.



SINTAX algorithm

See also
  sintax command
  Microbial taxonomy
  Cross-validation by identity

The SINTAX algorithm predicts the taxonomy of marker gene reads such as 16S or ITS. It is implemented in the sintax command.

Bootstrap confidence values are provided for all predicted ranks.

The algorithm is similar to the RDP Naive Bayesian Classifier algorithm except that k-mer similarity is used to identify the top taxonomy rather than Bayesian posteriors so there is no need for training.

Unlike the RDP Classifier, SINTAX does not require that the lowest ("training") rank be specified for all reference sequences which allows the use of large databases as a reference. However, I do not recommend using SILVA or Greengenes as a taxonomy reference because these databases have high error rates -- roughly one in five of the taxonomy annotations are wrong.