UPARSE: highly accurate OTU sequences from microbial amplicon reads

Nat Methods. 2013 Oct;10(10):996-8. doi: 10.1038/nmeth.2604. Epub 2013 Aug 18.


Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. 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. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.

MeSH terms

  • Algorithms
  • Databases, Genetic
  • Humans
  • Metagenomics
  • Microbiota / genetics*
  • Phylogeny*
  • RNA, Ribosomal, 16S / genetics*
  • Research Design
  • Sensitivity and Specificity
  • Software


  • RNA, Ribosomal, 16S