An analytical framework for optimizing variant discovery from personal genomes

Gareth Highnam, Jason J. Wang, Dean Kusler, Justin Zook, Vinaya Vijayan, Nir Leibovich and David Mittelman ()
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Gareth Highnam: Gene by Gene Ltd
Jason J. Wang: Gene by Gene Ltd
Dean Kusler: Gene by Gene Ltd
Justin Zook: National Institute of Standards and Technology
Vinaya Vijayan: Virginia Bioinformatics Institute, Virginia Tech
Nir Leibovich: Gene by Gene Ltd
David Mittelman: Gene by Gene Ltd

Nature Communications, 2015, vol. 6, issue 1, 1-6

Abstract: 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 .

Date: 2015
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DOI: 10.1038/ncomms7275

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