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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

makeudb_sintax command

The makeudb_tax command creates a UDB database file from sequences in a FASTA file. The database file is compatible with the sintax, usearch_global and usearch_local commands. Using a udb index make the database faster to load, but otherwise does not change the results.

See SINTAX reference data downloads page for available reference files.

You don't need to trim sequences to the same region as your reads / OTUs.

The sequence labels in the FASTA file must contain taxonomy annotations.

Example

usearch -makeudb_sintax rdp_16s.fa -output rdp_16s.udb