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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.

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.

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