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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.



SINAPS algorithm

See also
sinaps command
  SINAPS paper.

SINAPS (Simple Non-Bayesian Attribute Prediction Software) predict atrributes (traits) for a marker gene sequence. From an abstract perspective, SINAPS is essentially the same algorithm as SINTAX. A reference database is provided in which each marker gene sequence is annotated with the trait to be predicted. A random subset of words is extracted from the query sequence and used to find the reference database sequence (top hit) with most words in common. This process is repeated 100 times and the most frequently occurring top-hit trait is reported as the predicted trait for the query. The number of iterations in which that trait was the top hit is reported as the bootstrap confidence value.