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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.



UCHIME algorithm

See also
  Chimera formation
  Reproducibility of results
  Comparison of UCHIME and DECIPHER

UCHIME and UCHIME2 are algorithms for detecting chimeric sequences. See the UCHIME and UCHIME2 papers for details. Note that the accuracy results reported in the original UCHIME paper are highly over-optimistic due to unrelaistic benchmark design. This is explained in the UCHIME2 paper.

Stand-alone UCHIME[2] should not be used in OTU clustering or denoising pipelines because the cluster_otus and unoise3 commands have more effective chimera filters integrated into the algorithms. You will probably get much higher error rates, both false positives and false negatives, if you use UCHIME[2] as a stand-alone filtering step.