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Research Article

SHRiMP: Accurate Mapping of Short Color-space Reads

  • Stephen M. Rumble,

    Affiliations: Department of Computer Science, University of Toronto, Toronto, Ontario, Canada, Department of Computer Science, Stanford University, Stanford, California, United States of America

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  • Phil Lacroute,

    Affiliations: Department of Genetics, Stanford University, Stanford, California, United States of America, Department of Pathology, Stanford University, Stanford, California, United States of America

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  • Adrian V. Dalca,

    Affiliation: Department of Computer Science, University of Toronto, Toronto, Ontario, Canada

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  • Marc Fiume,

    Affiliation: Department of Computer Science, University of Toronto, Toronto, Ontario, Canada

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  • Arend Sidow,

    Affiliations: Department of Genetics, Stanford University, Stanford, California, United States of America, Department of Pathology, Stanford University, Stanford, California, United States of America

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  • Michael Brudno mail

    brudno@cs.toronto.edu

    Affiliations: Department of Computer Science, University of Toronto, Toronto, Ontario, Canada, Banting & Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada

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  • Published: May 22, 2009
  • DOI: 10.1371/journal.pcbi.1000386

Reader Comments (1)

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a question

Posted by fuyutao on 29 May 2009 at 21:00 GMT

In Figure 4, why is there no horizontal 'xover's ?

No competing interests declared.

RE: a question

brudus replied to fuyutao on 30 May 2009 at 03:01 GMT

Because the gap is in the read -- no color from the read gets generated, so no possibility of a sequencing error.

No competing interests declared.