clustermq enables efficient parallelization of genomic analyses

Michael Schubert*

*Bijbehorende auteur voor dit werk

    OnderzoeksoutputAcademicpeer review

    2 Citaten (Scopus)
    118 Downloads (Pure)

    Samenvatting

    Motivation: High performance computing (HPC) clusters play a pivotal role in large-scale bioinformatics analysis and modeling. For the statistical computing language R, packages exist to enable a user to submit their analyses as jobs on HPC schedulers. However, these packages do not scale well to high numbers of tasks, and their processing overhead quickly becomes a prohibitive bottleneck.

    Results: Here we present clustermq, an R package that can process analyses up to three orders of magnitude faster than previously published alternatives. We show this for investigating genomic associations of drug sensitivity in cancer cell lines, but it can be applied to any kind of parallelizable workflow.

    Originele taal-2English
    Pagina's (van-tot)4493-4495
    Aantal pagina's3
    TijdschriftBioinformatics
    Volume35
    Nummer van het tijdschrift21
    DOI's
    StatusPublished - 1-nov.-2019

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