sintax command
See also
SINTAX reference data downloads
Which taxonomy database should I use?
SINTAX algorithm
makeudb_sintax command
Can SINTAX predict species?
sintax_summary command
Cross-validation by identity
Taxonomy confidence measures
The sintax command uses the SINTAX algorithm to predict taxonomy for query sequences
in FASTA or FASTQ format.
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 with
bootstrap confidence values are written to the -tabbedout file. The first three fields are (1) query sequence label, (2) prediction with
bootstrap 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
References (please cite)
R.C. Edgar (2016), SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences, https://doi.org/10.1101/074161
• SINTAX taxonomy prediction algorithm
• Fast and simple method, accuracy comparable to RDP Classifier
R.C. Edgar (2018), Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences, PeerJ 6:e4652
• Cross-validation by identity, novel benchmark strategy enabling realistic accuracy estimates
• Genus accuracy of best methods is 50% on V4 sequences
• Recent algorithms do not improve on RDP Classifier or SINTAX
R.C. Edgar (2018), Taxonomy annotation and guide tree errors in 16S rRNA databases, PeerJ 6:e5030
• Approx. one in five SILVA and Greengenes taxonomy annotations are wrong
• SILVA and Greengenes trees have pervasive conflicts with type strain taxonomies
