Quality-filtering Vastly Improves Diversity Estimates From Illumina Amplicon Sequencing

Nat Methods. 2013 Jan;10(1):57-9. doi: 10.1038/nmeth.2276. Epub 2012 Dec 2.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biodiversity*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Quality Control*
  • Sequence Analysis, DNA / methods*