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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, unpaired

See also
  OTU / denoising pipeline
  Example pipelines with test data

This example shows the minimum commands you need to get from fixed-length unpaired reads to OTU sequences. In practice, you'll probably need to do more read preparation. The data has 4,259 reads of a mock community which generate ~21 OTUs. You need to set the environment variable $usearch to a valid command name for usearch, e.g. the full path name of the binary file.

Download commands and data
Reads: right-click on ex_min_reads.fq and click Save As.
Bash script: select all text below (ctrl+A) and copy/paste into a text editor, or right-click on ex_min.bash and click Save As.