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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Aizad, Sanna, Anjum, Ashiq and Sakellariou, Rizos 2017. Representing variant calling format as directed acyclic graphs to enable the use of cloud computing for efficient and cost effective genome analysis. IEEE. https://doi.org/10.1109/CCGRID.2017.116
AuthorsAizad, Sanna, Anjum, Ashiq and Sakellariou, Rizos
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.

KeywordsDirected acrylic graphs (DAG); Variant calling format (VCF); Bioinformatics; Genomics; Cloud computing; Directed graphs
Year2017
JournalProceedings of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing
PublisherIEEE
Digital Object Identifier (DOI)https://doi.org/10.1109/CCGRID.2017.116
Web address (URL)http://hdl.handle.net/10545/621949
hdl:10545/621949
ISBN9781509066117
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Publication dates13 Jul 2017
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Deposited10 Nov 2017, 11:41
ContributorsUniversity of Derby and University of Manchester
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