title: Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment.
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 of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics.petermac.org/treva/.
authors.affiliation: Bioinformatics, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; Department of Mechanical Engineering, The University of Melbourne, Parkville, VIC, Australia.
authors.forename: Jason
authors.initials: J
authors.lastname: Li
authors.affiliation: Bioinformatics, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: Maria A
authors.initials: MA
authors.lastname: Doyle
authors.affiliation: Department of Mechanical Engineering, The University of Melbourne, Parkville, VIC, Australia; YourGene Biosciences Australia, Southbank, VIC, Australia.
authors.forename: Isaam
authors.initials: I
authors.lastname: Saeed
authors.affiliation: Molecular Pathology Research and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: Stephen Q
authors.initials: SQ
authors.lastname: Wong
authors.affiliation: Victorian Melanoma Service, Alfred Hospital, Prahran, VIC, Australia; Department of Epidemiology and Preventive Medicine, Monash University, Clayton, VIC, Australia; Molecular Oncology Laboratory, Oncogenic Signaling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: Victoria
authors.initials: V
authors.lastname: Mar
authors.affiliation: Sarcoma Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia; Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: David L
authors.initials: DL
authors.lastname: Goode
authors.affiliation: Bioinformatics, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: Franco
authors.initials: F
authors.lastname: Caramia
authors.affiliation: Bioinformatics, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: Ken
authors.initials: K
authors.lastname: Doig
authors.affiliation: Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: Georgina L
authors.initials: GL
authors.lastname: Ryland
authors.affiliation: Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: Ella R
authors.initials: ER
authors.lastname: Thompson
authors.affiliation: Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: Sally M
authors.initials: SM
authors.lastname: Hunter
authors.affiliation: Department of Mechanical Engineering, The University of Melbourne, Parkville, VIC, Australia.
authors.forename: Saman K
authors.initials: SK
authors.lastname: Halgamuge
authors.affiliation: Bioinformatics, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: Jason
authors.initials: J
authors.lastname: Ellul
authors.affiliation: Molecular Pathology Research and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; Translational Genomics & Epigenomics Laboratory, Ludwig Institute for Cancer Research, Heidelberg, VIC, Australia.
authors.forename: Alexander
authors.initials: A
authors.lastname: Dobrovic
authors.affiliation: Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.
authors.forename: Ian G
authors.initials: IG
authors.lastname: Campbell
authors.affiliation: Bioinformatics division, The Walter and Eliza Hall Institute for Medical Research, Parkville, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia; Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: Anthony T
authors.initials: AT
authors.lastname: Papenfuss
authors.affiliation: Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia; Molecular Oncology Laboratory, Oncogenic Signaling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; Translational Research Laboratory, Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; Department of Medicine, St. Vincent's Hospital, Fitzroy, VIC, Australia; Department of Pathology, University of Melbourne, Parkville, VIC, Australia.
authors.forename: Grant A
authors.initials: GA
authors.lastname: McArthur
authors.affiliation: Translational Research Laboratory, Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; Department of Pathology, University of Melbourne, Parkville, VIC, Australia.
authors.forename: Richard W
authors.initials: RW
authors.lastname: Tothill
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D059472:Exome / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D008545:Melanoma / Q000235:genetics; D051379:Mice; D009154:Mutation / Q000235:genetics; D017422:Sequence Analysis, DNA; D014584:User-Computer Interface
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