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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.



-strand option

Required for nucleotide searches. Value must be set to plus or both.
-strand plus   Search for hits on the forward (plus) strand only. This is faster, so is recommended when the query sequences are known to be oriented on the same strand as the database.
-strand both   Search for hits on both the forward and reverse-complemented strands.