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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 validation data and commands

The HMP mock communities and sequencing protocols are described at HMPDACC.

Titanium reads
I used reads obtained with V3-V5 primers only.

Set Community Link to data
Even1P Even SRR053818
Even2P Even SRR072220
Even3P Even SRR072239
Stag1P Staggered SRR072221
Stag2P Staggered SRR072223
Stag3P Staggered SRR072237

MiSeq reads
The MiSeq reads are from Bokulich et al., 2013. Links to the data can be found via the QIIME resources page.

Software and commands

Package Version Commands
USEARCH 6.1.351_i86linux32 USEARCH command-lines.
mothur 1.27.0, Linux 64-bit mothur script.
QIIME 1.5.0 and 1.5.0-dev QIIME commands.