Skip to main content
eScholarship
Open Access Publications from the University of California

UC San Diego

UC San Diego Previously Published Works bannerUC San Diego

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

  • Author(s): Bokulich, Nicholas A
  • Subramanian, Sathish
  • Faith, Jeremiah J
  • Gevers, Dirk
  • Gordon, Jeffrey I
  • Knight, Rob
  • Mills, David A
  • Caporaso, J Gregory
  • et al.
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.

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Main Content
Current View