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    Representing variant calling format as directed acyclic graphs to enable the use of cloud computing for efficient and cost effective genome analysis

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    Authors
    Aizad, Sanna
    Anjum, Ashiq cc
    Sakellariou, Rizos
    Affiliation
    University of Derby
    University of Manchester
    Issue Date
    2017-07-13
    
    Metadata
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    Abstract
    Ever since the completion of the Human Genome Project in 2003, the human genome has been represented as a linear sequence of 3.2 billion base pairs and is referred to as the "Reference Genome". Since then it has become easier to sequence genomes of individuals due to rapid advancements in technology, which in turn has created a need to represent the new information using a different representation. Several attempts have been made to represent the genome sequence as a graph albeit for different purposes. Here we take a look at the Variant Calling Format (VCF) file which carries information about variations within genomes and is the primary format of choice for genome analysis tools. This short paper aims to motivate work in representing the VCF file as Directed Acyclic Graphs (DAGs) to run on a cloud in order to exploit the high performance capabilities provided by cloud computing.
    Citation
    Aizad, S. et al (2017) 'Representing variant calling format as directed acyclic graphs to enable the use of cloud computing for efficient and cost effective genome analysis', Proceedings of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, 14-17 May. DOI: 10.1109/CCGRID.2017.116
    Publisher
    IEEE
    Journal
    Proceedings of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing
    URI
    http://hdl.handle.net/10545/621949
    DOI
    10.1109/CCGRID.2017.116
    Additional Links
    http://ieeexplore.ieee.org/document/7973781/
    Type
    Meetings and Proceedings
    Language
    en
    ISBN
    9781509066117
    ae974a485f413a2113503eed53cd6c53
    10.1109/CCGRID.2017.116
    Scopus Count
    Collections
    Department of Electronics, Computing & Maths

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