USEARCH manual
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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.

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

 

USEARCH v11

Clustering

  UPARSE (OTU clustering for next-gen amplicon reads)
  UCLUST, general-purpose sequence clustering
  UCLUST sort order
  Abundance sorting
  Agglomerative clustering (single, complete and average linkage)
  Connected components (single-linkage clustering)
  Can UCLUST cluster metagenomics contigs?
  Clustering sequences using local alignment