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).

Staggered read pairs

If the paired read length is longer than the biological sequence in the construct, then the reads overflow into the sequencing primer and adapter sequences which bind the construct to the flow cell as shown below. I call this a "staggered" pair.

The fastq_mergepairs command discards any "overhangs" at the ends of the reads which do not align to the other read.