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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.



GG97 database download

See also
closed_ref command
  Closed-reference OTU assignent

GG97 is my name for the default closed-reference database used by QIIME. It is a subset of the Greengenes database (DeSantis et al. 2006) clustered at 97% identity. It is available from the QIIME github repository from the link below.


DeSantis, T.Z. et al., 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. AEM 72(7), pp.5069-72.