Creating a bit vector file for the search_16s command
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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

Creating a bit vector file for the search_16s command

See also
  search_16s command

Bit vector files are created by the udb2bitvec command. The recommended sequence database is the Greengenes 97% representative set. You should use the -wordlength 13 option of makeudb_usearch to create the udb file, as shown below.

usearch -makeudb_usearch gg97.fa -wordlength 13 -output gg97.udb

usearch -udb2bitvec gg97.udb -output gg97.bitvec