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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 QC: Contaminants

See also
  Quality control for OTU sequences

Contamint species can be introduced into your samples at every stage in the experimental protocol from sample collection to sequencing (e.g., residue on the flow-cell).

Detecting contaminants is difficult / impossible except in control samples e.g., distilled water, or a mock community. Control samples can be used to detect contaminants introduced in the stages from library preparation to sequencing. Note that cross-talk can also cause unexpected sequences in a control sample.