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Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.

ABSTRACT: High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and ?-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.

SUBMITTER: Bokulich NA 

PROVIDER: S-EPMC3531572 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature

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Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.

Bokulich Nicholas A NA   Subramanian Sathish S   Faith Jeremiah J JJ   Gevers Dirk D   Gordon Jeffrey I JI   Knight Rob R   Mills David A DA   Caporaso J Gregory JG  

Nature methods 20121202 1

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 d  ...[more]

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