DeeZ: reference-based compression by local assembly

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  1. 1

    Hach, F., Numanagic, I., Alkan, C. & Sahinalp, S.C. Bioinformatics 28, 3051–3057 (2012).

  2. 2

    Kozanitis, C., Saunders, C., Kruglyak, S., Bafna, V. & Varghese, G. J. Comput. Biol. 18, 401–413 (2011).

  3. 3

    Cox, A.J., Bauer, M.J., Jakobi, T. & Rosone, G. Bioinformatics 28, 1415–1419 (2012).

  4. 4

    Deorowicz, S. & Grabowski, S. Bioinformatics 27, 860–862 (2011).

  5. 5

    Jones, D.C., Ruzzo, W.L., Peng, X. & Katze, M.G. Nucleic Acids Res. 40, e171 (2012).

  6. 6

    Bonfield, J.K. & Mahoney, M.V. PLoS ONE 8, e59190 (2013).

  7. 7

    Bonfield, J.K. Bioinformatics 30, 2818–2819 (2014).

  8. 8

    Li, H. et al. Bioinformatics 25, 2078–2079 (2009).

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We thank the Natural Sciences and Engineering Research Council of Canada (NSERC) for the Discovery Frontiers “Cancer Genome Collaboratory” project, Discovery Grants program and Genome Canada (S.C.S.) and the Vanier Canada Graduate Scholarship program (I.N.) for funding this research. We also thank L. Stein, T. Beck and H. Babaran as well as L. Ding and R.J. Mashi for testing and benchmarking the performance of DeeZ. We thank J. Bonfield for helping us to improve DeeZ. We thank J. Dale, G. Asimenos and S. Batzoglou for support in the initial stages of this research.

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Correspondence to S Cenk Sahinalp.

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The authors declare no competing financial interests.

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Hach, F., Numanagic, I. & Sahinalp, S. DeeZ: reference-based compression by local assembly. Nat Methods 11, 1082–1084 (2014) doi:10.1038/nmeth.3133

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