Commands > Taxonomy
See alsoSINTAX reference data downloads
SINTAX algorithm
makeudb_sintax command
Can SINTAX predict species?
sintax_summary command
The sintax command uses the SINTAX algorithm to predict taxonomy for query sequences
in FASTA or FASTQ format. See SINTAX paper for details.
You can use the sintax_summary command to get a tabbed text file for making figures.
The search database must have taxonomy annotations. The makeudb_sintax command can be used to create a UDB database, which is faster to load. See SINTAX downloads page for available reference files in FASTA format.
Taxonomy predictions are written to the -tabbedout file. The first three fields are (1) query sequence label, (2) prediction with boostrap values and (3) strand. If the -sintax_cutoff option is given then predictions are written a second time after applying the confidence threshold, keeping only ranks with high enough confidence. On V4 reads, using a cutoff of 0.8 gives predictions with similar accuracy to RDP at 80% bootstrap cutoff.
The strand option must be specified.
Multithreading is supported.
Example
usearch -sintax reads.fastq -db 16s.udb -tabbedout reads.sintax
-strand both -sintax_cutoff 0.8