search_exact 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.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



search_exact command

See also
fastx_uniques command

The search_exact command searches for exact, full-length matches to a database sequence. The algorithm is faster than usearch_global, uses less memory, and is guaranteed to find all correct matches, i.e. there are no heuristics.

The underlying algorithm is the same as for the fastx_uniques command.

The query sequences may be in FASTA or FASTQ format.

The database file must be in FASTA format. Indexed (udb) databases are not supported.

The -strand option is required for nucleotide databases. If -strand both is specified, then reverse-complemented exact matches will also be reported.

Standard output file options are supported. For example, the -notmatched output file can be used to save query sequences that are not found in the database and the -dbnotmatched option can be used to save database sequences that are not present in the query set. This enables incremental updating of dereplicated sequence sets.

Multithreading is supported.


usearch -search_exact seqs.fa -db db.fa -blast6out matches.b6 -strand plus