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).

OTU table output files

Commands which support generating OTU tables understand the following options. The most commonly used commands are otutab and closed_ref.

-mapout filename
Tab-separated text file which maps reads to OTUs.
There is one read per line with two fields: the read label and the OTU identifier.

-otutabout filename
QIIME classic tabbed text format.

-biomout filename
BIOM v1.0 format (JSON). The biom utility can be used to convert to BIOM v2.1 format (HDF5).

-mothur_shared_out filename
Mothur "shared" file.