Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

Nicholas A. Bokulich; Sathish Subramanian; Jeremiah J. Faith; Dirk Gevers; Jeffrey I. Gordon; Rob Knight; David A. Mills; J. Gregory Caporaso

doi:10.1038/nmeth.2276

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

Nicholas A. Bokulich
, Sathish Subramanian
, Jeremiah J. Faith
, Dirk Gevers
, Jeffrey I. Gordon
, Rob Knight
, David A. Mills
, J. Gregory Caporaso

Research output: Contribution to journal › Article › peer-review

3909 Scopus citations

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.

Original language	English
Pages (from-to)	57-59
Number of pages	3
Journal	Nature Methods
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/nmeth.2276
State	Published - Jan 2013
Externally published	Yes

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10.1038/nmeth.2276

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@article{729054a979624e8186d0b6ff19c6412f,

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.",

author = "Bokulich, \{Nicholas A.\} and Sathish Subramanian and Faith, \{Jeremiah J.\} and Dirk Gevers and Gordon, \{Jeffrey I.\} and Rob Knight and Mills, \{David A.\} and Caporaso, \{J. Gregory\}",

note = "Funding Information: We thank G. Giannoukos (Broad Institute of MIT and Harvard), I. Rasolonjatovo (Illumina), M. Gebert (University of Colorado, Boulder) and L. Wegener Parfrey (University of Colorado, Boulder) for contributing mock community sequencing data used in this study, and S. Huse and A. Gonzalez for useful feedback and discussions of this manuscript. This work was supported in part by grants from the US National Institutes of Health (NIH DK78669 to J.I.G., NIH R01HD059127 to D.A.M. and NIH U54HG004969 to D.G.), the Juvenile Diabetes Research Fund (D.G.), the Crohn{\textquoteright}s and Colitis Foundation of America (J.I.G. and D.G.), and the Howard Hughes Medical Institute. N.A.B. was supported by the 2012–2013 Dannon Probiotics Fellow Program (The Dannon Company) and a Wine Spectator scholarship.",

year = "2013",

month = jan,

doi = "10.1038/nmeth.2276",

language = "English",

volume = "10",

pages = "57--59",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

number = "1",

}

TY - JOUR

T1 - Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

AU - Bokulich, Nicholas A.

AU - Subramanian, Sathish

AU - Faith, Jeremiah J.

AU - Gevers, Dirk

AU - Gordon, Jeffrey I.

AU - Knight, Rob

AU - Mills, David A.

AU - Caporaso, J. Gregory

N1 - Funding Information: We thank G. Giannoukos (Broad Institute of MIT and Harvard), I. Rasolonjatovo (Illumina), M. Gebert (University of Colorado, Boulder) and L. Wegener Parfrey (University of Colorado, Boulder) for contributing mock community sequencing data used in this study, and S. Huse and A. Gonzalez for useful feedback and discussions of this manuscript. This work was supported in part by grants from the US National Institutes of Health (NIH DK78669 to J.I.G., NIH R01HD059127 to D.A.M. and NIH U54HG004969 to D.G.), the Juvenile Diabetes Research Fund (D.G.), the Crohn’s and Colitis Foundation of America (J.I.G. and D.G.), and the Howard Hughes Medical Institute. N.A.B. was supported by the 2012–2013 Dannon Probiotics Fellow Program (The Dannon Company) and a Wine Spectator scholarship.

PY - 2013/1

Y1 - 2013/1

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/84871979584

U2 - 10.1038/nmeth.2276

DO - 10.1038/nmeth.2276

M3 - Article

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VL - 10

SP - 57

EP - 59

JO - Nature Methods

JF - Nature Methods

IS - 1

ER -

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

Abstract

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