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Efficient Indexed Alignment of Contigs to Optical Maps

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Algorithms in Bioinformatics (WABI 2014)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8701))

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Abstract

Since its emergence almost 20 years ago (Schwartz et al., Science 1995), optical mapping has undergone a transition from laboratory technique to commercially available data generation method. In line with this transition, it is only relatively recently that optical mapping data has started to be used for scaffolding contigs and assembly validation in large-scale sequencing projects — for example, the goat (Dong et al., Nature Biotech. 2013) and amborella (Chamala et al., Science 2013) genomes. One major hurdle to the wider use of optical mapping data is the efficient alignment of in silico digested contigs to an optical map. We develop Twin to tackle this very problem. Twin is the first index-based method for aligning in silico digested contigs to an optical map. Our results demonstrate that Twin is an order of magnitude faster than competing methods on the largest genome. Most importantly, it is specifically designed to be capable of dealing with large eukaryote genomes and thus is the only non-proprietary method capable of completing the alignment for the budgerigar genome in a reasonable amount of CPU time.

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Author information

Authors and Affiliations

  1. Department of Computer Science, Colorado State University, Fort Collins, CO, USA

    Martin D. Muggli & Christina Boucher

  2. Department of Computer Science, University of Helsinki, Finland

    Simon J. Puglisi

Authors
  1. Martin D. Muggli
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  2. Simon J. Puglisi
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  3. Christina Boucher
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Editor information

Editors and Affiliations

  1. David R. Cheriton School of Computer Science, University of Waterloo, ON, Canada

    Dan Brown

  2. Institute of Microbiology and Genetics, Department of Bioinformatics, University of Göttingen, Germany, Goldschmidtstr. 1, 37077, Göttingen, Germany

    Burkhard Morgenstern

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Muggli, M.D., Puglisi, S.J., Boucher, C. (2014). Efficient Indexed Alignment of Contigs to Optical Maps. In: Brown, D., Morgenstern, B. (eds) Algorithms in Bioinformatics. WABI 2014. Lecture Notes in Computer Science(), vol 8701. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-44753-6_6

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  • DOI: https://doi.org/10.1007/978-3-662-44753-6_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-44752-9

  • Online ISBN: 978-3-662-44753-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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