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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
 New in v11 

otutab_xtalk command

Identify and filter cross-talk in an OTU table using the UNCROSS2 algorithm.

The -minxtscore option specifies the score threshold. Default 0.1.

If there are mock community control samples, you can use the mockhits option to specify a tabbed text file reporting hits of OTU sequences to the mock community reference database. This enables more reliable identification of cross-talk into mock samples. The tabbed file should have three fields: #1. OTU label, #2. reference label, #3. percent identity. This format can generated by using the following options of the usearch_global command: -userout mockhits.txt -userfields query+target+pctid.

The -report option specifies a text file name for a report.

The -htmlout option specifies an HTML file name. This generates a web page for the OTU table where entries are colored according to their cross-talk score (see example on right).

The -otutabout option specifies the name of an OTU table output file in QIIME classic format. Counts with a score at or above the minxtscore threshold are set to zero.

Example

usearch -otutab_xtalk otutab.txt -report xtalk_report.txt \
  -htmlout xtalk.html -otutabout otutabx.txt
 


Reference (please cite)
R.C. Edgar (2018), UNCROSS2: identification of cross-talk in 16S rRNA OTU tables, https://doi.org/10.1101/400762
  • Cross-talk rate is approx. 1% in many Illumina datasets

  • Cross-talk can cause false positive core microbiome

  • UNCROSS2 algorithm for filtering cross-talk