SAVANT GENOME BROWSER Marc Fiume Department of Computer Science University of Toronto

High Throughput Sequencing HTS machines can read billions of nucleotide bases per run interpretation and analysis challenge many separate tools for computational and visualization Savant Genome Browser -

Tools for Genomic Data Analysis ToolCostComputationVisualization Read Alignment e.g. Bowtie, BWA FreeYN File Format Conversion e.g. Galaxy, SAMTools FreeYN Other Comand-line Tools e.g. Genetic Variation Discovery, Comparitive Genomics, etc. FreeYN UCSC Genome BrowserFreeNY Integrative Genomics ViewerFreeNY GBrowseFreeNY CLC Genomics Workbench$$$YY Savant Genome Browser - substantial disconnect between the processes of computational analysis and visualization

Tools for Genomic Data Analysis ToolCostComputationVisualization Read Alignment e.g. Bowtie, BWA FreeYN File Format Conversion e.g. Galaxy, SAMTools FreeYN Other Comand-line Tools e.g. Genetic Variation Discovery, Comparitive Genomics, etc. FreeYN UCSC Genome BrowserFreeNY Integrative Genomics ViewerFreeNY GBrowseFreeNY CLC Genomics Workbench$$$YY Savant Genome BrowserFreeYY Savant Genome Browser - substantial disconnect between the processes of computational analysis and visualization

Savant Genome Browser platform for integrated visual analysis of genomic data feature-rich genome browser computationally extensible via plugin framework Savant Genome Browser - CategoryFeatures Data FormatsFASTA, SAM/BAM, BED, WIG, GFF, tab-delimited Speed and EfficiencyFast data access Scalable to very large input files Small memory footprint OthersBookmarking favorite locations Tabular data view Locking overview tracks Novel representation of paired-end reads making structural variations easy to identify Operating SystemsWorks on Windows, Linux, and Mac

FEATURE DEMONSTRATION Savant Genome Browser - INTERFACE HTS READ ALIGNMENTS EXAMPLE PLUGIN: SNP FINDER

Plugin Framework provides ability to extend Savant beyond its core functionalities for programmers: platform for simple development and deployment of various programs for users: allows one mix and match modules to perform customized visual analysis Savant Genome Browser -

Plugin API Savant Genome Browser - Range get/set range zoom in/out listen for range change Bookmarks add / remove bookmark(s) navigate to bookmark get bookmark(s) listen for bookmarks change Tracks add / remove track(s) get track data (in-range or whole genome) change colour scheme change visualization mode Other get position of mouse on genome capture screenshot rich collection of functions to get data, perform computations, and create custom visualizations UI edit menus draw custom graphics

On-the-fly SNP Finder Savant Genome Browser - listen for range change get track data in range DETECT SNPs add bookmark draw custom graphics user input : range change

Savant Plugins SNP Finder Bookmark Intersection Continuous Track Statistics Bookmark Player Table View we encourage plugin submissions, which can be done through the Savant website Savant Genome Browser -

CONCLUSIONS & FUTURE WORK Savant Genome Browser -

Conclusions Savant is a platform for integrated visualization and analysis of genomic data stand-alone genome browser standard features: e.g. file formats, navigation novel features: e.g. table view, matepair mode, etc. computationally extensible through plugin framework makes interpretation and analysis of genomic data easier and more efficient Savant Genome Browser -

Future work external datasources e.g. SQL database, 1000 Genomes Project Online DB improve and increase data format support grow user and developer community Savant Genome Browser -

Acknowledgements Savant Team Marc Fiume, Vanessa Williams, Andrew Brook, Michael Brudno Usability and Testing Alyssa Rosenzweig, Mohit Jain, Akhil Mathur, Paul Medvedev, Misko Dzamba, Nilgun Donmez, Daniel Lister, Andy Pang, Elango Cheran Savant Genome Browser -

Try out Savant for yourself PosterMain conference #J17 Live demo on Sunday, 12:40 – 2:30 Websitehttp://compbio.cs.toronto.edu/savant Savant Genome Browser -