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Bokulich, Nicholas A; Subramanian, Sathish; Faith, Jeremiah J; Gevers, Dirk; Gordon, Jeffrey I; Knight, Rob; Mills, David A; Caporaso, J Gregory
Nature methods, 01/2013, Volume: 10, Issue: 1Journal Article
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.
