New Generations: Sequencing Machines and Their Computational Challenges
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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.
Keywordsgenome sequencing new generation sequencing read mapping optical mapping sequence assembly Eulerian graphs
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- Harris T D, Buzby P R, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch J W, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake S R, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Single-molecule DNA sequencing of a viral genome. Science, 2008, 320(5872): 106-109.CrossRefGoogle Scholar
- Jett J H, Keller R A, Martin J C, Marrone B L, Moyzis R K, Ratliff R L, Seitzinger N K, Shera E B, Stewart C C. Highspeed DNA sequencing: An approach based upon fluorescence detection of single molecules. J. Biomol. Struct. Dyn., 1989, 7(2): 301-309.Google Scholar
- Waterman M S. Introduction to Computational Biology. Chapman & Hall, 1995.Google Scholar
- Kececioglu J D. Exact and approximation algorithms for DNA sequence reconstruction [Ph.D. Dissertation]. University of Arizona, Tucson, USA, 1992.Google Scholar
- Venter J C, Adams M D, Myers E W et al. The sequence of the human genome. Science, 2001, 291: 1304-1351.Google Scholar
- Myers E W. The fragment assembly string graph. Bioinformatics, 2005, 21(Suppl. 2): ii79-ii85, doi:10.1093/bioinformatics/bti7114.
- Pevzner P A, Tang H. Fragment assembly with doublebarreled data. Bioinformatics, 2001, 17(Suppl. 1): S225-S233.Google Scholar
- Zhou S, Herschleb J, Schwartz D C. A Single Molecule System forWhole Genome Analysis. New Methods for DNA Sequencing, Mitchelson K R (ed)., Amsterdam: Elsevier, 2007.Google Scholar
- Zhou S, Pape L, Schwartz D C. Optical Sequencing: Acquisition from Mapped Single Molecule Templates. Next Generation Genome Sequencing: Towards Personalized Medicine, Janitz M (ed.), 2008, Weinheim: Wiley-VCH Verlag & Co., pp.133-149.Google Scholar