title: An analytical framework for optimizing variant discovery from personal genomes.
abstract: The standardization and performance testing of analysis tools is a prerequisite to widespread adoption of genome-wide sequencing, particularly in the clinic. However, performance testing is currently complicated by the paucity of standards and comparison metrics, as well as by the heterogeneity in sequencing platforms, applications and protocols. Here we present the genome comparison and analytic testing (GCAT) platform to facilitate development of performance metrics and comparisons of analysis tools across these metrics. Performance is reported through interactive visualizations of benchmark and performance testing data, with support for data slicing and filtering. The platform is freely accessible at http://www.bioplanet.com/gcat.
authors.affiliation: Gene by Gene Ltd, Houston, Texas 77008, USA.
authors.forename: Gareth
authors.initials: G
authors.lastname: Highnam
authors.affiliation: Gene by Gene Ltd, Houston, Texas 77008, USA.
authors.forename: Jason J
authors.initials: JJ
authors.lastname: Wang
authors.affiliation: Gene by Gene Ltd, Houston, Texas 77008, USA.
authors.forename: Dean
authors.initials: D
authors.lastname: Kusler
authors.affiliation: Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Zook
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA.
authors.forename: Vinaya
authors.initials: V
authors.lastname: Vijayan
authors.affiliation: Gene by Gene Ltd, Houston, Texas 77008, USA.
authors.forename: Nir
authors.initials: N
authors.lastname: Leibovich
authors.affiliation: 1] Gene by Gene Ltd, Houston, Texas 77008, USA [2] Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA.
authors.forename: David
authors.initials: D
authors.lastname: Mittelman
mesh_terms: D019985:Benchmarking; D014644:Genetic Variation; D023281:Genomics; D006801:Humans; D012984:Software