Video talks on 16S data analysis posted.

URMAP ultra-fast read mapper posted (paper).

~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).

Taxonomy prediction is <50% accurate for 16S V4 sequences (paper).

97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4 (paper).

makeudb_sintax command

The makeudb_tax command creates a UDB database file from sequences in a FASTA file. The database file is compatible with the sintax, usearch_global and usearch_local commands. Using a udb index make the database faster to load, but otherwise does not change the results.

See SINTAX reference data downloads page for available reference files.

You don't need to trim sequences to the same region as your reads / OTUs.

The sequence labels in the FASTA file must contain taxonomy annotations.

Example

usearch -makeudb_sintax rdp_16s.fa -output rdp_16s.udb