UPARSE: highly accurate OTU sequences from microbial amplicon reads

RC Edgar - Nature methods, 2013 - nature.com
Nature methods, 2013nature.com
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.
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.
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