SAVANT GENOME BROWSER Marc Fiume Department of Computer

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 - http: //compbio. cs. toronto. edu/savant/

Tools for Genomic Data Analysis Tool Cost Computation Visualization Read Alignment Free Y N File Format Conversion Free Y N Other Comand-line Tools Free Y N UCSC Genome Browser Free N Y Integrative Genomics Viewer Free N Y GBrowse Free N Y CLC Genomics Workbench $$$ Y Y e. g. Bowtie, BWA e. g. Galaxy, SAMTools e. g. Genetic Variation Discovery, Comparitive Genomics, etc. • substantial disconnect between the processes of computational analysis and visualization Savant Genome Browser - http: //compbio. cs. toronto. edu/savant/

Tools for Genomic Data Analysis Tool Cost Computation Visualization Read Alignment Free Y N File Format Conversion Free Y N Other Comand-line Tools Free Y N UCSC Genome Browser Free N Y Integrative Genomics Viewer Free N Y GBrowse Free N Y CLC Genomics Workbench $$$ Y Y Savant Genome Browser Free Y Y e. g. Bowtie, BWA e. g. Galaxy, SAMTools e. g. Genetic Variation Discovery, Comparitive Genomics, etc. • substantial disconnect between the processes of computational analysis and visualization Savant Genome Browser - http: //compbio. cs. toronto. edu/savant/

Savant Genome Browser • platform for integrated visual analysis of genomic data • feature-rich genome browser • computationally extensible via plugin framework Category Features Data Formats FASTA, SAM/BAM, BED, WIG, GFF, tab-delimited Speed and Efficiency Fast data access Scalable to very large input files Small memory footprint Others Bookmarking favorite locations Tabular data view Locking overview tracks Novel representation of paired-end reads making structural variations easy to identify Operating Systems Works on Windows, Linux, and Mac Savant Genome Browser - http: //compbio. cs. toronto. edu/savant/

FEATURE DEMONSTRATION INTERFACE HTS READ ALIGNMENTS EXAMPLE PLUGIN: SNP FINDER Savant Genome Browser - http: //compbio. cs. toronto. edu/savant/

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 - http: //compbio. cs. toronto. edu/savant/

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

On-the-fly SNP Finder user input : range change listen for range change get track data in range DETECT SNPs add bookmark draw custom graphics Savant Genome Browser - http: //compbio. cs. toronto. edu/savant/

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 - http: //compbio. cs. toronto. edu/savant/

CONCLUSIONS & FUTURE WORK Savant Genome Browser - http: //compbio. cs. toronto. edu/savant/

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 - http: //compbio. cs. toronto. edu/savant/

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 - http: //compbio. cs. toronto. edu/savant/

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 - http: //compbio. cs. toronto. edu/savant/

Try out Savant for yourself Poster Website Email Main conference #J 17 Live demo on Sunday, 12: 40 – 2: 30 http: //compbio. cs. toronto. edu/savant@cs. toronto. edu Savant Genome Browser - http: //compbio. cs. toronto. edu/savant/