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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.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 

USEARCH v11
 New in v11 

nbc_tax command

See also
  sintax command
  Taxonomy
  Which taxonomy database should I use?
  Naive Bayesian Classifier algorithm
  makeudb_sintax command
  sintax_summary command
  Cross-validation by identity

The nbc_tax command is an implementation of the RDP Naive Bayesian Classifier algorithm (Wang et al. 2007). Predictions by nbc_tax are very similar to the Java implementation provided by RDP; differences are consistent with the randomness of bootstrapping so I believe that the results are equivalent for all practical purposes..

Taxonomy predictions are written to the -tabbedout file. The first three fields are (1) query sequence label, (2) prediction with bootstrap values and (3) strand. If the -sintax_cutoff option is given then predictions are written a second time after applying the confidence threshold, keeping only ranks with high enough confidence. The sintax_summary command can be used to generate a summary report.

The strand option must be specified.

Multithreading is supported.

Example

usearch -nbc_tax otus.fa -db ref16s.fa -strand plus -tabbedout tax.txt

Reference
Wang,Q. et al. (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. AEM 73, 5261-7.
 


References (please cite)
R.C. Edgar (2016), SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences, https://doi.org/10.1101/074161
  • SINTAX taxonomy prediction algorithm

  • Fast and simple method, accuracy comparable to RDP Classifier


R.C. Edgar (2018), Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences, PeerJ 6:e4652
  • Cross-validation by identity, novel benchmark strategy enabling realistic accuracy estimates

  • Genus accuracy of best methods is 50% on V4 sequences

  • Recent algorithms do not improve on RDP Classifier or SINTAX


R.C. Edgar (2018), Taxonomy annotation and guide tree errors in 16S rRNA databases, PeerJ 6:e5030
  • Approx. one in five SILVA and Greengenes taxonomy annotations are wrong

  • SILVA and Greengenes trees have pervasive conflicts with type strain taxonomies