UPARSE: highly accurate OTU sequences from microbial amplicon reads

• Published in: Nature methods Vol. 10; no. 10; pp. 996 - 998
• Main Author: Edgar, Robert C
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.10.2013; Nature Publishing Group
• Subjects: 631/114/794; 631/208/212/2142; 631/326/2565/2142; Algorithms; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical Engineering/Biotechnology; brief-communication; Community structure; Databases, Genetic; DNA sequencing; Gene amplification; Gene expression; Genetic markers; Genomics; Humans; Life Sciences; Metagenomics; Methods; Microbiota - genetics; Nucleotide sequencing; Phylogeny; Proteomics; Research Design; RNA, Ribosomal, 16S - genetics; Sensitivity and Specificity; Software; United States
• ISSN: 1548-7091; 1548-7105; 1548-7105
• DOI: 10.1038/nmeth.2604

To determine microbial community structure, the UPARSE software extracts operational taxonomic unit (OTU) representative sequences with high accuracy on the basis of amplified marker-gene sequences. 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.