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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.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



userout option

The userout option specifies a tabbed text output file with field names specified by the -userfields option. For example, the following will give the same output as -blast6out hits.m8:

 usearch -ublast reads.fastq -db proteins.fa -evalue 0.01 -userout hits.m8
   -userfields query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits