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Journal of Computer Science and Technology

, Volume 25, Issue 1, pp 3-9

New Generations: Sequencing Machines and Their Computational Challenges

  • David C. SchwartzAffiliated withLaboratory for Molecular and Computational Genomics, Department of Chemistry and Laboratory of Genetics, University of Wisconsin-Madiso Email author 
  • , Michael S. WatermanAffiliated withDepartment of Biological Sciences, University of Southern CaliforniaDepartment of Automation, Tsinghua University

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Abstract

New generation sequencing systems are changing how molecular biology is practiced. The widely promoted $1000 genome will be a reality with attendant changes for healthcare, including personalized medicine. More broadly the genomes of many new organisms with large samplings from populations will be commonplace. What is less appreciated is the explosive demands on computation, both for CPU cycles and storage as well as the need for new computational methods. In this article we will survey some of these developments and demands.

Keywords

genome sequencing new generation sequencing read mapping optical mapping sequence assembly Eulerian graphs