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Divide and Conquer Computation of the Multi-string BWT and LCP Array

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Sailing Routes in the World of Computation (CiE 2018)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10936))

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Abstract

Indexing huge collections of strings, such as those produced by the widespread sequencing technologies, heavily relies on multi-string generalizations of the Burrows-Wheeler Transform (BWT) and the Longest Common Prefix (LCP) array, since solving efficiently both problems are essential ingredients of several algorithms on a collection of strings.

In this paper we explore lightweight and parallel computational strategies for building the BWT and LCP array. We design a novel algorithm based on a divide and conquer approach that leads to a simultaneous and parallel computation of multi-string BWT and LCP array.

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Authors and Affiliations

  1. DISCo, University of Milano-Bicocca, Milan, Italy

    Paola Bonizzoni, Gianluca Della Vedova, Serena Nicosia, Yuri Pirola, Marco Previtali & Raffaella Rizzi

Authors
  1. Paola Bonizzoni
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  2. Gianluca Della Vedova
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  3. Serena Nicosia
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  4. Yuri Pirola
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  5. Marco Previtali
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  6. Raffaella Rizzi
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Corresponding author

Correspondence to Marco Previtali .

Editor information

Editors and Affiliations

  1. Kiel University, Kiel, Germany

    Florin Manea

  2. Queens College, CUNY, Queens, New York, USA

    Russell G. Miller

  3. Kiel University, Kiel, Germany

    Dirk Nowotka

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Bonizzoni, P., Della Vedova, G., Nicosia, S., Pirola, Y., Previtali, M., Rizzi, R. (2018). Divide and Conquer Computation of the Multi-string BWT and LCP Array. In: Manea, F., Miller, R., Nowotka, D. (eds) Sailing Routes in the World of Computation. CiE 2018. Lecture Notes in Computer Science(), vol 10936. Springer, Cham. https://doi.org/10.1007/978-3-319-94418-0_11

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  • DOI: https://doi.org/10.1007/978-3-319-94418-0_11

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-94417-3

  • Online ISBN: 978-3-319-94418-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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