Introduction

As high-throughput sequencing continues to increase in speed and throughput, routine clinical and industrial application draws closer. These 'production' settings will require enhanced quality monitoring and quality control to optimize output and reduce costs. We developed SeqControl, a framework for predicting sequencing quality and coverage using a set of 15 metrics describing overall coverage, coverage distribution, basewise coverage and basewise quality. Using whole-genome sequences of 27 prostate cancers and 26 normal references, we derived multivariate models that predict sequencing quality and depth. SeqControl robustly predicted how much sequencing was required to reach a given coverage depth (area under the curve (AUC) = 0.993), accurately classified clinically relevant formalin-fixed, paraffin-embedded samples, and made predictions from as little as one-eighth of a sequencing lane (AUC = 0.967). These techniques can be immediately incorporated into existing sequencing pipelines to monitor data quality in real time. SeqControl is available at http://labs.oicr.on.ca/Boutros-lab/software/SeqControl/.

Publications

  1. SeqControl: process control for DNA sequencing.
    Cite this
    Chong LC, Albuquerque MA, Harding NJ, Caloian C, Chan-Seng-Yue M, de Borja R, Fraser M, Denroche RE, Beck TA, van der Kwast T, Bristow RG, McPherson JD, Boutros PC, 2014-10-01 - Nature methods

Credits

  1. Lauren C Chong
    Developer

    Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Canada

  2. Marco A Albuquerque
    Developer

    Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Canada

  3. Nicholas J Harding
    Developer

    Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Canada

  4. Cristian Caloian
    Developer

    Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Canada

  5. Michelle Chan-Seng-Yue
    Developer

    Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Canada

  6. Richard de Borja
    Developer

    Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Canada

  7. Michael Fraser
    Developer

    Department of Pathology, University Health Network, Canada

  8. Robert E Denroche
    Developer

    Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Canada

  9. Timothy A Beck
    Developer

    Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Canada

  10. Theodorus van der Kwast
    Developer

    Department of Pathology, University Health Network, Canada

  11. Robert G Bristow
    Developer

    1] Ontario Cancer Institute, University Health Network, Canada

  12. John D McPherson
    Developer

    1] Department of Medical Biophysics, University of Toronto, Canada

  13. Paul C Boutros
    Investigator

    1] Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Canada

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Summary
AccessionBT000358
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl, R
User InterfaceTerminal Command Line
Download Count0
Country/RegionCanada
Submitted ByPaul C Boutros