Parsimony score options
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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

Parsimony score options

 See also
  uparse_ref
  cluster_otus

 
Option Default Description
-uparse_match 0.0 Parsimony score for matching pair of letters.
-uparse_mismatch -1.0 Parsimony score for mismatch.
-uparse_break -3.0 Parsimony score for chimeric breakpoint.