Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Methods 10, 57–59. doi: 10.1038/nmeth.2276

High-throughput sequencing has revolutionized microbial ecology, but read quality remains a significant barrier to accurate taxonomy assignment and alpha 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 from, and facilitating interpretation of Illumina sequencing results. Recent advances in high-throughput, short-amplicon sequencing are revolutionizing efforts to describe microbial diversity within and across complex biomes, including the human body1 and Earth’s biosphere2. The greater sequence coverage and lower per-base cost of the Illumina GAIIx, HiSeq, and MiSeq instruments aids this progress over more expensive, lower-coverage platforms. Given unknown sequencing error rates for amplicon data generated by these rapidly evolving instruments and changing chemistries, and the potentia