title: UPARSE: highly accurate OTU sequences from microbial amplicon reads.
abstract: 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.
authors: Independent Investigator, Tiburon, California, USA.
authors: Robert C
authors: RC
authors: Edgar
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D006801:Humans; D056186:Metagenomics; D064307:Microbiota / Q000235:genetics*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012107:Research Design; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S
references: FEMS Microbiol Ecol. 2012 Dec;82(3):666-77
references: 22738186
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D13-25
references: 22140104
references: Nature. 2012 Jun 13;486(7402):207-14
references: 22699609
references: Environ Microbiol. 2010 Jul;12(7):1889-98
references: 20236171
references: Genome Res. 2011 Mar;21(3):494-504
references: 21212162
references: Appl Environ Microbiol. 2006 Jul;72(7):5069-72
references: 16820507
references: BMC Bioinformatics. 2012 Feb 14;13:31
references: 22333067
references: BMC Bioinformatics. 2011 Jan 28;12:38
references: 21276213
references: PLoS One. 2011;6(12):e27310
references: 22194782
references: Nat Methods. 2013 Jan;10(1):57-9
references: 23202435
references: Nature. 2012 Aug 2;488(7409):86-90
references: 22859206
references: Bioinformatics. 2011 Aug 15;27(16):2194-200
references: 21700674
references: Nature. 2012 Jun 13;486(7402):215-21
references: 22699610
references: Nat Methods. 2010 Sep;7(9):668-9
references: 20805793
references: Nat Methods. 2009 Sep;6(9):639-41
references: 19668203
references: Nat Methods. 2010 May;7(5):335-6
references: 20383131