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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.



Pipeline example: minimal, paired

See also
  OTU / denoising pipeline

This example shows the minimum commands you need to get from overlapping paired reads to OTUs and denoised (ZOTU) sequences. In practice, you'll probably need to do more read preparation. There are 4,259 reads of a mock community which generate ~21 OTUs and ~22 ZOTUs. You need to set the environment variable $usearch to the name (or path) for your usearch binary file.

Download commands and data
Reads: right-click on ex_min2_reads.tar.gz and click Save As. Use tar -zxvf ex_min2_reads.tar.gz to extract.
Bash script: select all text below (ctrl+A) and copy/paste into a text editor, or right-click on ex_min2.bash and click Save As.