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_usearch command

The makeudb_usearch command creates a UDB database file from sequences in a FASTA file. Index parameters are set to defaults for usearch_global and usearch_local. These defaults can be overridden by specifying index parameters on the command line.

The name of the UDB file is specified by the -output option.

Example

usearch -makeudb_usearch db.fasta -output db.udb

usearch -makeudb_usearch db.fasta -output db.udb -wordlength 12 -dbstep 4