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

1199 Scopus citations


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
Issue number1
StatePublished - Jan 2013


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., Mills, D. A., & 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