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An analytical framework for optimizing variant discovery from personal genomes



Justin M. Zook, Gareth Highnam, Jason Wang, Dean Kusler, Vinaya Vijayan, Nir Leibovich, David Mittelman


The standardization and performance testing of analysis tools is a prerequisite to widespread adoption of high-throughput sequencing, particularly in the clinic. However, performance testing is currently complicated by the paucity of standards and comparison metrics, as well as the heterogeneity in sequencing platforms, applications, and protocols. We have developed the open and collaborative 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
Nature Methods


DNA sequencing, genomics, bioinformatics, Reference Materials


Zook, J. , Highnam, G. , Wang, J. , Kusler, D. , Vijayan, V. , Leibovich, N. and Mittelman, D. (2015), An analytical framework for optimizing variant discovery from personal genomes, Nature Methods, [online], (Accessed June 14, 2024)


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Created February 25, 2015, Updated November 10, 2018