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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

search_global command

 
Comprehensive database search. All database sequences are aligned to the query, no index is used. Alignments are global. Much slower than usearch_global for large datasets; mostly useful for ad hoc queries on small datasets. Sensitive to arbitrarily low identities.

An identity threshold must be specified using the -id option.

A database file must be specified using the -db option.

The -strand option is required for nucleotide databases.

Nucleotide, protein and translated searches are supported.

See also:
  Standard output file options
 
Accept options
  Weak hits
  Termination options
  Multithreading
  Alignment parameters

Example

usearch -search_global query.fasta -db db.fasta -id 0.9 -alnout results.aln