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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.



usearch_local command

Search for one (default) or a few high-identity hits to a database using the USEARCH algorithm. Alignments are local. To get more than one hit, increase -maxaccepts. The USEARCH algorithm is generally best suited for global alignments, but local searches may sometimes be appropriate and effective. This is the case when the local alignments cover a large enough fraction of both the query and target sequence that the common word count between the full-length sequences correlates with similarity in the region. Increasing -maxrejects may improve sensitivity when this assumption holds less well.

Usually, ublast should be used instead of usearch_local.

An identity threshold must be specified using the -id option. An E-value threshold may also be specified.

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
  Indexing options
  Masking options
  Alignment parameters
  Alignment heuristics


usearch -usearch_local query.fasta -db proteins.udb -id 0.8 -alnout results.aln
usearch -usearch_local query.fasta -db ESTs.fasta -id 0.9  -evalue 1e-6 \
  -userout hits.txt -userfield query+target+evalue+id