Journal
NATURE METHODS
Volume 10, Issue 1, Pages 57-U11Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/NMETH.2276
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Funding
- US National Institutes of Health [NIH DK78669, NIH R01HD059127, NIH U54HG004969]
- Juvenile Diabetes Research Fund
- Crohn's and Colitis Foundation of America
- Howard Hughes Medical Institute
- Dannon Probiotics Fellow Program (The Dannon Company)
- Wine Spectator scholarship
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High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable 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 and facilitating interpretation of Illumina sequencing results.
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