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 QC: PhiX spike-in

A PhiX spike-in is used for Illumina sequencing of amplicon libraries for 16S and other marker genes. Then, PhiX is typically found in around 5% of the raw reads. Often, these are filtered before you see the FASTQ files, but not always, and third-party PhiX filtering software may not be accurate. In usearch, PhiX search is based on the ublast algorithm, and is very sensitive.

The search_phix command can be used for searching and the filter_phix command can be used for filtering.