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sintax command
Commands > Taxonomy

See also
 
SINTAX reference data downloads
  Which taxonomy database should I use?
  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. See also Which database should I use?

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