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How to classify 16S data with UTAX

1. Download the 16S reference files and extract them from the archive using tar -zxvf. The archive contains a FASTA database with full-length sequences plus pre-trained taxconfs files for shorter segmenets (500nt, 250nt and 120nt).

2. Choose the taxconfs file for length closest to your sequences.

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 500.tc

4. Run the utax command or cluster_otus_utax command:

usearch -utax reads.fastq -db tax.udb -utaxout utax.txt -strand both