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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.



makeudb_usearch command


The makeudb_usearch command creates a UDB database file from sequences in a FASTA file. Index parameters are set to defaults for usearch_global and usearch_local. These defaults can be overridden by specifying index parameters on the command line.

The name of the UDB file is specified by the -output option.


usearch -makeudb_usearch db.fasta -output db.udb

usearch -makeudb_usearch db.fasta -output db.udb -wordlength 12 -dbstep 4