sintax command
See also
Should I use UTAX or SINTAX? Which database?
SINTAX reference data downloads
SINTAX algorithm
makeudb_sintax command
Can SINTAX predict species?
The sintax command uses the SINTAX algorithm to predict taxonomy for query sequences in FASTA or FASTQ format. See SINTAX paper for details.
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 the query sequence label, prediction with boostrap values and the 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