1. Download the ITS reference filesand extract them from the archive using tar -zxvf. The archive contains a FASTA database with full-length sequences plus pre-trained taxconfs files for full-legnth ITS and the ITS1 and ITS2 regions.
2. Choose the taxconfs file for your region.
3. Make the UDB file using the makeudb_utax command (it is ok to use full-length reference sequences with parameters for shorter sequences):
usearch -makeudb_utax refdb.fa -output refdb.udb -taxconfsin its1.tc
4. Run the utax command or cluster_otus_utax command:
usearch -utax reads.fastq -db tax.udb -utaxout
utax.txt -strand both