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).

cluster quality and sequence identity

USEARCH uses the BLAST definition of sequence identity. Through version 5, USEARCH used the CD-HIT definition by default.

For a given alignment, BLAST identity <= CD-HIT identity. This is because BLAST counts gaps as differences, but CD-HIT sometimes does not. Insertions and deletions are generally less probable than substitutions. Therefore, gaps should count as least as much as substitutions as a measure of evolutionary distance, and the BLAST definition is more biologically realistic.