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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.



open reading frames

An open reading frame (ORF) is a segment of a nucleotide sequence that begins with a start codon, ends with a stop codon and is long enough to code for a protein. In USEARCH, the minimum number of amino acid codons in an ORF is set by the -mincodons option, default value 20.

With a nucleotide query sequence and amino acid database, USEARCH performs a translated search. ORFs are identified in the nucleotide sequence, and each ORF is treated as a separate query with its own termination conditions. This is because a single nucleotide sequence may span more than one gene.