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Scaling Whole Exome sequencing using workflows on the cloud

Lookup NU author(s): Dr Jacek Cala, Dr Paolo Missier

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Abstract

Copyright © (2014) by Universita Reggio Calabria & Centro di Competenza (ICT-SUD) All rights reserved.Whole exome / genome sequencing (WES/WGS) is poised to become a cornerstone of genetic testing for diagnosis in clinical practice, at population scale. The Cloud-e-Genome project, started in late 2013, addresses three architectural requirements in support of WES-based diagnosis, namely (i) scalability of the storage and computing resources required to extract variants from sequences, (ii) flexibility in the design and evolution of WES processing pipelines, and (iii) reproducibility of the results. Our approach involves using a scientific workflow model to program the pipelines for flexibility, deploying the workflows on the Azure cloud for scalability, and recording the provenance of workflow execution, for reproduciblity. In this discussion paper we elaborate on our design choices, the associated challenges, and the expected benefits.


Publication metadata

Author(s): Cala J, Missier P

Editor(s): Sergio Greco, Antonio Picariello

Publication type: Conference Proceedings (inc. Abstract)

Publication status: Published

Conference Name: 22nd Italian Symposium on Advanced Database Systems (SEBD)

Year of Conference: 2014

Pages: 201-208

Online publication date: 01/11/2014

Acceptance date: 01/01/1900

Publisher: Universita Reggio Calabria and Centro di Competenza (ICT-SUD)

URL: http://www.proceedings.com/23358.html

Library holdings: Search Newcastle University Library for this item

ISBN: 9781634391450


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