Journal article

Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment

Jason Li, Maria A Doyle, Isaam Saeed, Stephen Q Wong, Victoria Mar, David L Goode, Franco Caramia, Ken Doig, Georgina L Ryland, Ella R Thompson, Sally M Hunter, Saman K Halgamuge, Jason Ellul, Alexander Dobrovic, Ian G Campbell, Anthony T Papenfuss, Grant A McArthur, Richard W Tothill

PLOS ONE | PUBLIC LIBRARY SCIENCE | Published : 2014

Abstract

Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment o..

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