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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

-dbaccelpct option

 
Controls the fraction of unmasked unique seeds that are indexed by the makeudb_search or makeudb_ublast command, expressed as a percentage. Value must be between 0 and 100, default is 100. With values < 100, the database will be smaller and searches will be faster, at the expense of a loss in sensitivity. Note that the database size scaling is not linear, so with -dbaccel 90 the database might be half as big.

This option can be useful for reducing the memory requirements of a search. To improve speed, it it is generally better to use the -accel option which uses query-specific statistics to prioritize seeds. With -dbaccel, averaged statistics are used which tend to have lower sensitivity for a given query. With indexes for usearch_global and usearch_local, the -dbstep option is usually preferred for reducing memory use.