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, J. Gregory Caporaso

Research output: Contribution to journalArticlepeer-review

3050 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
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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