title: Cpipe: a shared variant detection pipeline designed for diagnostic settings.
abstract: The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines have been built from the ground up with clinical genomics in mind. Here we present Cpipe, a pipeline designed specifically for clinical genetic disease diagnostics. Cpipe was developed by the Melbourne Genomics Health Alliance, an Australian initiative to promote common approaches to genomics across healthcare institutions. As such, Cpipe has been designed to provide fast, effective and reproducible analysis, while also being highly flexible and customisable to meet the individual needs of diverse clinical settings. Cpipe is being shared with the clinical sequencing community as an open source project and is available at http://cpipeline.org.
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia.
authors.forename: Simon P
authors.initials: SP
authors.lastname: Sadedin
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia ; Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Harriet
authors.initials: H
authors.lastname: Dashnow
authors.affiliation: Genetic Medicine, Royal Melbourne Hospital, Parkville, VIC 3052 Australia.
authors.forename: Paul A
authors.initials: PA
authors.lastname: James
authors.affiliation: Population Health and Immunity Division, The Walter and Eliza Hall Institute, Royal Parade, Parkville, VIC 3052 Australia ; Department of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC 3010 Australia ; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Melanie
authors.initials: M
authors.lastname: Bahlo
authors.affiliation: CSIRO, Digital Productivity Flagship, 11 Julius Av, 2113, Sydney, Australia.
authors.forename: Denis C
authors.initials: DC
authors.lastname: Bauer
authors.affiliation: Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Andrew
authors.initials: A
authors.lastname: Lonie
authors.affiliation: Genomic Medicine, Centre for Translational Pathology, Department of Pathology, The University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Lunke
authors.affiliation: Victorian Clinical Genetics Service, Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia ; Melbourne Genomics Health Alliance, Melbourne, Australia.
authors.forename: Ivan
authors.initials: I
authors.lastname: Macciocca
authors.affiliation: CSIRO Food and Nutrition Flagship, North Ryde, NSW 2113 Australia.
authors.forename: Jason P
authors.initials: JP
authors.lastname: Ross
authors.affiliation: Australian Genome Research Facility, The Walter and Eliza Hall Institute, Royal Parade, Parkville, VIC 3050 Australia.
authors.forename: Kirby R
authors.initials: KR
authors.lastname: Siemering
authors.affiliation: Victorian Clinical Genetics Service, Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia.
authors.forename: Zornitza
authors.initials: Z
authors.lastname: Stark
authors.affiliation: Victorian Clinical Genetics Service, Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia ; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Susan M
authors.initials: SM
authors.lastname: White
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia ; Genomic Medicine, Centre for Translational Pathology, Department of Pathology, The University of Melbourne, Melbourne, VIC 3010 Australia ; Victorian Clinical Genetics Service, Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia.
authors.forename: Graham
authors.initials: G
authors.lastname: Taylor
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia ; Victorian Clinical Genetics Service, Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia ; Melbourne Genomics Health Alliance, Melbourne, Australia ; Department of Medicine, The University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Clara
authors.initials: C
authors.lastname: Gaff
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia.
authors.forename: Alicia
authors.initials: A
authors.lastname: Oshlack
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia ; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010 Australia ; Melbourne Genomics Health Alliance, Melbourne, Australia ; Walter and Eliza Hall Institute, Parkville, VIC 3052 Australia.
authors.forename: Natalie P
authors.initials: NP
authors.lastname: Thorne