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.
Published Web Locationhttps://doi.org/10.1038/nmeth.2276
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.