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PAGANtec: OpenMP Parallel Error Correction for Next-Generation Sequencing Data

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OpenMP: Heterogenous Execution and Data Movements (IWOMP 2015)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 9342))

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Abstract

Next-generation sequencing techniques reduced the cost of sequencing a genome rapidly, but came with a relatively high error rate. Therefore, error correction of this data is a necessary task before assembly can take place. Since the input data is huge and error correction is compute intensive, parallelizing this work on a modern shared-memory system can help to keep the runtime feasible. In this work we present PAGANtec, a tool for error correction of next-generation sequencing data, based on the novel PAGAN graph structure. PAGANtec was parallelized with OpenMP and a performance analysis and tuning was done. The analysis led to the awareness, that OpenMP tasks are a more suitable paradigm for this work than traditional work-sharing.

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Author information

Authors and Affiliations

  1. JARA – High-Performance Computing, IT Center, RWTH Aachen University, Aachen, Germany

    Markus Joppich, Dirk Schmidl & Torsten Kuhlen

  2. Institute for Botany and Molecular Genetics, RWTH Aachen University, Aachen, Germany

    Markus Joppich, Anthony M. Bolger & Björn Usadel

  3. Institute for Informatics, Ludwig-Maximilians-Universität Munich, Munich, Germany

    Markus Joppich

Authors
  1. Markus Joppich
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  2. Dirk Schmidl
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  3. Anthony M. Bolger
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  4. Torsten Kuhlen
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  5. Björn Usadel
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Corresponding author

Correspondence to Markus Joppich .

Editor information

Editors and Affiliations

  1. RWTH Aachen University, Aachen, Germany

    Christian Terboven

  2. Lawrence Livermore National Laboratory, Livermore, California, USA

    Bronis R. de Supinski

  3. RWTH Aachen University, Aachen, Germany

    Pablo Reble

  4. University of Houston, Houston, California, USA

    Barbara M. Chapman

  5. RWTH Aachen University, Aachen, Germany

    Matthias S. Müller

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© 2015 Springer International Publishing Switzerland

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Joppich, M., Schmidl, D., Bolger, A.M., Kuhlen, T., Usadel, B. (2015). PAGANtec: OpenMP Parallel Error Correction for Next-Generation Sequencing Data. In: Terboven, C., de Supinski, B., Reble, P., Chapman, B., Müller, M. (eds) OpenMP: Heterogenous Execution and Data Movements. IWOMP 2015. Lecture Notes in Computer Science(), vol 9342. Springer, Cham. https://doi.org/10.1007/978-3-319-24595-9_1

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  • DOI: https://doi.org/10.1007/978-3-319-24595-9_1

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-24594-2

  • Online ISBN: 978-3-319-24595-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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