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Performance Optimization for the Trinity RNA-Seq Assembler

In: Tools for High Performance Computing 2015

Author

Listed:
  • Michael Wagner

    (Barcelona Supercomputing Center
    Technische Universität Dresden, Center for Information Services and High Performance Computing)

  • Ben Fulton

    (Scientific Applications and Performance Tuning Indiana University)

  • Robert Henschel

    (Scientific Applications and Performance Tuning Indiana University)

Abstract

Utilizing the enormous computing resources of high performance computing systems is anything but a trivial task. Performance analysis tools are designed to assist developers in this challenging task by helping to understand the application behavior and identify critical performance issues. In this paper we share our efforts and experiences in analyzing and optimizing Trinity, a well-established framework for the de novo reconstruction of transcriptomes from RNA-seq reads. Thereby, we try to reflect all aspects of the ongoing performance engineering: the identification of optimization targets, the code improvements resulting in 22 % overall runtime reduction, as well as the challenges we encountered getting there.

Suggested Citation

  • Michael Wagner & Ben Fulton & Robert Henschel, 2016. "Performance Optimization for the Trinity RNA-Seq Assembler," Springer Books, in: Andreas Knüpfer & Tobias Hilbrich & Christoph Niethammer & José Gracia & Wolfgang E. Nagel & Michael (ed.), Tools for High Performance Computing 2015, chapter 0, pages 29-40, Springer.
    • Handle: RePEc:spr:sprchp:978-3-319-39589-0_3
    DOI: 10.1007/978-3-319-39589-0_3
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