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Last updated 19 Jul 2024


High-accuracy, high-throughput OTU clustering
UPARSE is a method for generating clusters (OTUs) from next-generation 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 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 and mothur 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].