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12-Jun-2018 New paper shows that ~20% of taxonomy annotations are wrong in SILVA and Greengenes.

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 97% threshold is wrong -- OTUs should be 99% full-length 16S, 100% for V4.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 


 
 
 
 
 
 
 
Getting started
  What's new in v10
  Installation
  Command line
  Tutorials and lecture slides
  Papers and citing USEARCH

Commands
  All commands
  Algorithms
  Commands by category
      search, clustering, fasta/q files
      trees & distance matrices
      OTU commands
  Command-line options

Support
  Technical support
  Known bugs
 

 
Marker gene metagenomics (16S, ITS...)
  OTU / denoising analysis
  Quality control for OTUs
  Example scripts with test data
  Diversity and taxonomy analysis
  OTU tables

Topics in sequence analysis
 
OTU analysis, clustering methods,
  taxonomy, diversity analysis,
  next-gen reads

Old manuals 
  Version 9.2
  Version 8.1
  Version 7
  Version 6