A fantastic new paper out on the UPARSE pipeline and algorithm for cleaning and clustering OTUs in microbial diversity work, from Robert C Edgar. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods.

Paradigm shift?

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2604.html

“UPARSE works by quality-filtering reads, trimming them to a fixed length, optionally discarding singleton reads and then clustering the remaining reads. Clustering uses UPARSE-OTU, a novel ‘greedy’ algorithm that performs chimera filtering and OTU clustering simultaneously—unlike previously developed methods, which perform chimera filtering as a separate step, if at all.”