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Nat Methods. 2013 Jan;10(1):57-9. doi: 10.1038/nmeth.2276. Epub 2012 Dec 2.

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.

Author information

1
Department of Viticulture and Enology, University of California, Davis, Davis, California, USA.

Abstract

High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and α-diversity assessment for microbial communities. We demonstrate that high-quality read length and abundance are the primary factors differentiating correct from erroneous reads produced by Illumina GAIIx, HiSeq and MiSeq instruments. We present guidelines for user-defined quality-filtering strategies, enabling efficient extraction of high-quality data and facilitating interpretation of Illumina sequencing results.

PMID:
23202435
PMCID:
PMC3531572
DOI:
10.1038/nmeth.2276
[Indexed for MEDLINE]
Free PMC Article

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