Graphical Applications for Visualization and Analysis of Genotype Data Sets

Plant geneticists require a new generation of software tools to interrogate the increasingly high volume data sets that are being generated by high-throughput SNP platforms, genotyping-by-sequencing and other comparable genotyping technologies. Within the Seeds of Discovery project (http://www.seedsofdiscovery.org) we find that we are increasingly using data visualization to support and complement our analysis through the applications that we have developed. These include Flapjack to visualize graphical genotypes from extensive SNP and GBS data sets, and CurlyWhirly to visualize spatial xyz plots such as those obtained from principal coordinates analysis. Although standalone, these applications also seamlessly integrate with the wider suite of tools forming part of this project (for example Germinate that handles and presents the storage of genetic resources and experimental data) so that information can be easily passed from database to analysis to visualization and back again.

Written in Java with support for multiple desktop platforms (Windows, OS X and Linux), our applications are freely available in 32 and 64-bit formats from http://bioinf.hutton.ac.uk/flapjack and http://bioinf.hutton.ac.uk/curlywhirly. They are designed for high-performance, real-time visualization and exploration of large data sets, have easy installation with no complex software dependencies, and provide intuitive, geneticist-friendly graphical user interfaces.

This work is supported through the Mexican Government MasAgro programme.