title: 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 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.
authors.affiliation: Department of Viticulture and Enology, University of California, Davis, Davis, California, USA.
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Bokulich
authors.forename: Sathish
authors.initials: S
authors.lastname: Subramanian
authors.forename: Jeremiah J
authors.initials: JJ
authors.lastname: Faith
authors.forename: Dirk
authors.initials: D
authors.lastname: Gevers
authors.forename: Jeffrey I
authors.initials: JI
authors.lastname: Gordon
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.forename: David A
authors.initials: DA
authors.lastname: Mills
authors.forename: J Gregory
authors.initials: JG
authors.lastname: Caporaso
mesh_terms: D044822:Biodiversity; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods*