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mrsFAST: a cache-oblivious algorithm for short-read mapping

Nature Methods volume 7, pages 576–577 (2010)Cite this article

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In addition to single-nucleotide variations and small insertions-deletions (indels), larger-sized structural variations (for example, insertions, deletions, inversions, segmental duplications and copy-number polymorphisms) contribute to human genetic diversity. In almost all recent structural variation discovery (SVD) studies, short reads from a donor genome have been mapped to a reference genome as a first step. The accuracy of such an SVD study is directly correlated to the accuracy of this mapping step, which also provides the main computational bottleneck of the SVD study.

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Acknowledgements

We thank the following funding agencies for providing support: Genome British Columbia Science Opportunities Fund (to S.C.S. and I.B.), Mathematics of Information Technology and Complex Systems Accelerate Program (to F. Hach and Fe. Hormozdiari), National Sciences and Engineering Research Council Discovery Grant Program (to S.C.S.), Simon Fraser University Community Endowment Trust Fund (to S.C.S.), Howard Hughes Medical Institute (to E.E.E.), National Institutes of Health (HG004120 to E.E.E.). We thank A. Ghane and V. Kazempour for their help with the use of the OProfile tool.

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Authors and Affiliations

  1. School of Computing Science, Simon Fraser University, Burnaby, Canada

    Faraz Hach, Fereydoun Hormozdiari, Farhad Hormozdiari, Inanc Birol & S Cenk Sahinalp

  2. Department of Genomics, University of Washington School of Medicine, Seattle, Washington, USA

    Can Alkan, Evan E Eichler & S Cenk Sahinalp

  3. Howard Hughes Medical Institute, Seattle, Washington, USA

    Can Alkan & Evan E Eichler

  4. Genome Sciences Center, British Columbia Cancer Agency, Vancouver, Canada

    Inanc Birol

Authors
  1. Faraz Hach
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  2. Fereydoun Hormozdiari
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  3. Can Alkan
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  4. Farhad Hormozdiari
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  5. Inanc Birol
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  6. Evan E Eichler
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  7. S Cenk Sahinalp
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Corresponding author

Correspondence to S Cenk Sahinalp.

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Hach, F., Hormozdiari, F., Alkan, C. et al. mrsFAST: a cache-oblivious algorithm for short-read mapping. Nat Methods 7, 576–577 (2010). https://doi.org/10.1038/nmeth0810-576

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  • DOI: https://doi.org/10.1038/nmeth0810-576

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