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

  • Markus JoppichEmail author
  • Dirk Schmidl
  • Anthony M. Bolger
  • Torsten Kuhlen
  • Björn Usadel
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9342)

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.

Keywords

Error Correction Graph Structure Transcriptome Assembly Transactional Memory Load Imbalance 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Markus Joppich
    • 1
    • 2
    • 3
    Email author
  • Dirk Schmidl
    • 1
  • Anthony M. Bolger
    • 2
  • Torsten Kuhlen
    • 1
  • Björn Usadel
    • 2
  1. 1.JARA – High-Performance Computing, IT CenterRWTH Aachen UniversityAachenGermany
  2. 2.Institute for Botany and Molecular GeneticsRWTH Aachen UniversityAachenGermany
  3. 3.Institute for InformaticsLudwig-Maximilians-Universität MunichMunichGermany

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