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Primer and assay design
UPARSE is an OTU clustering algorithm published in Nature Methods.

Benchmark results
UPARSE generates OTUs that are far superior to state-of-the-art methods including QIIME, mothur and AmpliconNoise on mock community tests. OTU representative sequences are more accurate predictions of biological sequences, and the number of OTUs is much close to the number of species.

See UPARSE pipeline.

The UPARSE algorithm is implemented in USEARCH v7 and later. To get the software, go to the USEARCH download page.

Edgar, R.C. (2013) UPARSE: Highly accurate OTU sequences from microbial amplicon reads,
Nature Methods [Pubmed:23955772dx.doi.org/10.1038/nmeth.2604].