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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.



search_local command

Comprehensive database search. All database sequences are aligned to the query, no index is used. Alignments are local. Much slower than usearch_local or ublast for large datasets; mostly useful for ad hoc queries on small datasets. A hit will be found only if there is at least one exact matching word of length -hspw, which defaults to 3 for proteins and 5 for nucleotides, or the -fulldp option is specified (see alignment heuristics).

An E-value threshold must be specified using the -evalue 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
  Alignment parameters


usearch -search_local query.fasta -db db.fasta -evalue 10 -alnout results.aln