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).

UCHIME vs. UPARSE

See also
Chimera benchmark home
UPARSE-OTU algorithm with chimera filtering (cluster_otus command).

UCHIME and UPARSE compared for OTU clustering
Below is Fig 1(a) from the UPARSE paper. Magenta segments in the pie chart show the fraction of chimeric OTUs generated by several algorithms on a mock community test. The QIIME and mothur pipelines used UCHIME for chimera detection. Notice that even after UCHIME filtering, about 50% of the OTUs generated by QIIME and mothur are chimeric, while UPARSE successfully filters all chimeras from Illumina reads and leaves only one chimeric OTU with 454 reads.