• DocumentCode
    640167
  • Title

    Optimal DNA shotgun sequencing: Noisy reads are as good as noiseless reads

  • Author

    Motahari, Amin ; Ramchandran, Kannan ; Tse, David ; Nan Ma

  • Author_Institution
    Dept. of Electr. Eng. & Comput. Sci., Univ. of California, Berkeley, Berkeley, CA, USA
  • fYear
    2013
  • fDate
    7-12 July 2013
  • Firstpage
    1640
  • Lastpage
    1644
  • Abstract
    We establish the fundamental limits of DNA shotgun sequencing under noisy reads. We show a surprising result: for the i.i.d. DNA model, noisy reads are as good as noiseless reads, provided that the noise level is below a certain threshold which can be surprisingly high. As an example, for a uniformly distributed DNA sequence and a symmetric substitution noisy read channel, the threshold is as high as 19%.
  • Keywords
    DNA; genomics; DNA model; noiseless reads; noisy reads; optimal DNA shotgun sequencing; Assembly; DNA; Greedy algorithms; Noise; Noise level; Noise measurement; Sequential analysis;
  • fLanguage
    English
  • Publisher
    ieee
  • Conference_Titel
    Information Theory Proceedings (ISIT), 2013 IEEE International Symposium on
  • Conference_Location
    Istanbul
  • ISSN
    2157-8095
  • Type

    conf

  • DOI
    10.1109/ISIT.2013.6620505
  • Filename
    6620505