Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

Nicholas A. Bokulich, Sathish Subramanian, Jeremiah J. Faith, Dirk Gevers, Jeffrey I. Gordon, Rob Knight, David A. Mills, James G Caporaso

Research output: Contribution to journalArticle

1105 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)57-59
Number of pages3
JournalNature Methods
Volume10
Issue number1
DOIs
StatePublished - Jan 2013

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Taxonomies
Ecology
Throughput
Guidelines
Data Accuracy

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology

Cite this

Bokulich, N. A., Subramanian, S., Faith, J. J., Gevers, D., Gordon, J. I., Knight, R., ... Caporaso, J. G. (2013). Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods, 10(1), 57-59. https://doi.org/10.1038/nmeth.2276

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. / Bokulich, Nicholas A.; Subramanian, Sathish; Faith, Jeremiah J.; Gevers, Dirk; Gordon, Jeffrey I.; Knight, Rob; Mills, David A.; Caporaso, James G.

In: Nature Methods, Vol. 10, No. 1, 01.2013, p. 57-59.

Research output: Contribution to journalArticle

Bokulich, NA, Subramanian, S, Faith, JJ, Gevers, D, Gordon, JI, Knight, R, Mills, DA & Caporaso, JG 2013, 'Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing', Nature Methods, vol. 10, no. 1, pp. 57-59. https://doi.org/10.1038/nmeth.2276
Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods. 2013 Jan;10(1):57-59. https://doi.org/10.1038/nmeth.2276
Bokulich, Nicholas A. ; Subramanian, Sathish ; Faith, Jeremiah J. ; Gevers, Dirk ; Gordon, Jeffrey I. ; Knight, Rob ; Mills, David A. ; Caporaso, James G. / Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. In: Nature Methods. 2013 ; Vol. 10, No. 1. pp. 57-59.
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