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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

sinaps command

See also
  SINAPS algorithm

The sinaps command predicts an attribute (trait) for a sequence by searching a database of sequences annotated with known values for the attribute. For example, the attribute could be the SSU copy number specified by a copynr= annotation in the database sequence labels. The value of the attribute can be any string of characters allowed as the value of an annotation.

The name of the attribute is specified by the -attr option, which must match the name used in the annotations.

By default, confidence is estimated by boostrapping. If confidence is not needed, this feature can be turned off for faster execution by using the -noboot option. The -boot_subset option (default 32) specifies the number of words in the subset used for bootstrapping and the -boots option (default 100) specifies the number of bootstrap iterations.

The -strand option is required. The value can be plus or both.

Output is written in tabbed text format to the -tabbedout file. Fields are: query label, predicted attribute, bootstrap confidence (number of iterations where this attribute was predicted), strand (+ or -) and the label of the top database hit.

Example

usearch -sinaps seqs.fa -db copynr.udb -attr copynr -tabbedout copynr.txt -strand both