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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.



mosaic option

Terminate search if the query sequence is covered by hits. The sequence sequence is considered to be covered if the longest segment which is not aligned is less than 16 letters long. The size of the segment can be set by the -mosaic_minseg option (default 16).

The effect of this option is similar to -cover_query. However, cover_query is a post-processing step after hits have been found, while -mosaic is a termination condition. This means that -cover_query may find report stronger hits than -mosaic, depending on the other options specified.