OTU benchmarks

USEARCH performance home page

OTU benchmark results.

Benchmarking OTU methods
It is difficult to benchmark a OTU clustering method because there is no consensus in the microbiology community on how to define an OTU or how to measure accuracy. Several attempts have been made in the literature, but in my opinion the methods are not convincing and some papers have serious problems. Here are some slides describing challenges in constructing and benchmarking OTUs. I doubt that it is possible to definitively resolve these problems. I think it would probably be more productive to frame 16S sequence analysis problems in terms of the phylogenetic tree of the 16S gene. Contact me if you would like to discuss this further or if you are doing your own benchmarking, in which case I would appreciate the opportunity to discuss the best way to use USEARCH in the context of your tests.