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Research Article

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

  • John Martin,

    Affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America

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  • Sean Sykes,

    Affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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  • Sarah Young,

    Affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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  • Karthik Kota,

    Affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America

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  • Ravi Sanka,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

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  • Nihar Sheth,

    Affiliation: Virginia Commonwealth University, Center for Study of Biological Complexity, Richmond, Virginia, United States of America

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  • Joshua Orvis,

    Affiliation: Insitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

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  • Erica Sodergren,

    Affiliations: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America

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  • Zhengyuan Wang,

    Affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America

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  • George M. Weinstock,

    Affiliations: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America

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  • Makedonka Mitreva mail

    mmitreva@watson.wustl.edu

    Affiliations: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America

    X
  • Published: June 13, 2012
  • DOI: 10.1371/journal.pone.0036427
  • Published in PLOS ONE

About the Authors

John Martin, Karthik Kota, Erica Sodergren, Zhengyuan Wang, George M. Weinstock, Makedonka Mitreva
The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
Sean Sykes, Sarah Young
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
Ravi Sanka
J. Craig Venter Institute, Rockville, Maryland, United States of America
Nihar Sheth
Virginia Commonwealth University, Center for Study of Biological Complexity, Richmond, Virginia, United States of America
Joshua Orvis
Insitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
Erica Sodergren, George M. Weinstock, Makedonka Mitreva
Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America

Corresponding Author

Email: mmitreva@watson.wustl.edu

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: MM GMW ES. Analyzed the data: JM SS SY KK RS NS JO ZW. Wrote the paper: JM GMW MM.