Note: I am working on an major update of utax for v8.1.
The utax command uses the UTAX algorithm to assign taxonomy to input sequences in FASTA or FASTQ format.
A reference database is required which must have taxonomy annotations specified by a tax=nnn; field in the FASTA label.
The database may be in FASTA or UDB format. Using UDB reduces the time and memory required to load the database, but requires the extra step of running makeudb_usearch.
A taxonomy tree file must be specified using the -tt option.
A taxconfs file is specified using the -taxconfs option. If you don't have a taxconfs file for your region, then you can use -utax_rawscore, which will write scores in place of P-values. It is then up to you to decide on a reasonable score cutoff at each level of interest.
See UTAX downloads page for available reference files.
Output is written to the utaxout file.
No alignments are created, so standard output files such as alnout and blast6out are not supported. If you want to review alignments to the reference database, then you can use usearch_global, or usearch_local if there may be non-biological sequences such as barcodes or adapters in the query sequences.
The strand option is not supported; searches are always performed on both strands.
Example
usearch -utax reads.fq -db 16s.udb -taxconfs
16s.tc -tt 16s.tt -utaxout results.txt