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Building a GATK-Based Tool for Methylation Analysis in Next-Generation Bisulfite Sequencing Experiments

  • Daniel Glez-Peña
  • Osvaldo Graña
  • Florentino Fdez-Riverola
  • David G. Pisano
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 93)

Abstract

Bisulfite sequencing is a technique that can be combined with next-generation sequencing approaches to analyze DNA methylation patterns in a genome wide scale. The GATK framework is a new Java framework for fast-developing NGS applications including capabilities for automatic shared-memory parallelization. This work presents the design and initial performance results of a methylation caller for next-generation bisultife sequencing based on the GATK framework.

Keywords

DNA methylation next-generation sequencing bisulfite sequencing GATK 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Daniel Glez-Peña
    • 1
  • Osvaldo Graña
    • 2
  • Florentino Fdez-Riverola
    • 1
  • David G. Pisano
    • 2
  1. 1.ESEI: Escuela Superior de Ingeniería InformáticaUniversity of Vigo, Edificio PolitécnicoOurenseSpain
  2. 2.Bioinformatics Unit, Structural Biology and BioComputing ProgrammeSpanish National Cancer Research Centre (CNIO)MadridSpain

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