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Last updated 12 Oct 2015

High-accuracy, high-throughput OTU clustering
UPARSE is a method for generating clusters (OTUs) from next-generating sequencing reads of marker genes such as 16S rRNA, the fungal ITS region and the COI gene. The clustering method itself is the UPARSE-OTU algorithm, implemented as the cluster_otus command in USEARCH. To run UPARSE in practice, you need to run a pipeline of scripts and USEARCH commands.

Benchmark tests
According to results published in Nature Methods, 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 are much closer to the number of species.

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