Journal of Computer Science and Technology

, Volume 25, Issue 1, pp 3–9

New Generations: Sequencing Machines and Their Computational Challenges

Survey

DOI: 10.1007/s11390-010-9300-x

Cite this article as:
Schwartz, D.C. & Waterman, M.S. J. Comput. Sci. Technol. (2010) 25: 3. doi:10.1007/s11390-010-9300-x

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 sequencingnew generation sequencingread mappingoptical mappingsequence assemblyEulerian graphs

Copyright information

© Springer 2010

Authors and Affiliations

  1. 1.Laboratory for Molecular and Computational Genomics, Department of Chemistry and Laboratory of GeneticsUniversity of Wisconsin-MadisoWisconsinU.S.A.
  2. 2.Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesU.S.A.
  3. 3.Department of AutomationTsinghua UniversityBeijingChina