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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.




Getting started
  What's new in v11
  Command line

Command reference
  All commands
  Commands by category

Documentation topics
  All topics
  Browse topics by category

Parameters and options
Output files for search and clustering
  Accept options (which hits to report)
  Termination options (when to stop searching)
  Alignment heuristics
  Alignment parameters (gap penalties etc.)
  Sequence database index parameters

  Papers and how to cite USEARCH
OTU and denoising analysis for 16S, ITS etc.
  Recommended procedures
  Example scripts and tutorials
  Errors and biases in amplicon sequencing

Old manuals
Version 10
  Version 9.2
  Version 8.1
  Version 7
  Version 6

  Technical support
  Known bugs