SAVANT GENOME BROWSERMarc FiumeDepartment of Computer ScienceUniversity of Toronto

Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

Challenge in Genome Informatics• genomic data is generated in high volumes• interpretation and analysis challenge

• many different tools have been developed for computation and visualization

Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

HTS data analysis pipelineTool Cost Computational Visualization

Read Alignment e.g. Bowtie, BWA

Free Y N

File Format Conversion e.g. Galaxy, SAMTools

Free Y N

Other Comand-line Toolse.g. Genetic Variation Discovery, Comparitive Genomics, etc.

Free Y N

UCSC Genome Browser Free N Y

Integrative Genomics Viewer Free N Y

GBrowse Free N Y

CLC Genomics Workbench $$$ Y Y

• substantial disconnect between the processes of computational analysis and visualization

Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

Tools for Genomic Data AnalysisTool Cost Computation Visualization

Read Alignment e.g. Bowtie, BWA

Free Y N

File Format Conversion e.g. Galaxy, SAMTools

Free Y N

Other Comand-line Toolse.g. Genetic Variation Discovery, Comparitive Genomics, etc.

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

• 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

Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

Summary of Features

• FASTA, BAM (local and remote), BED, WIG, GFF, tab-delimited

Data Format Support

• very fast data access (<1s); small memory footprint (<250 MB)

Speed and Interactivity

• pack, squish for BED and GFF tracks; mismatch, SNP, matepair modes for BAM tracks

Visualization Modes

• enables powerful analytic extensions to the browser

Plugin Framework

• sessions, bookmarking of interesting regions, track locking, data selection

Extras

• works on all major operating systems

System Requirements

FEATURE DEMONSTRATION

Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

INTERFACEHTS READ ALIGNMENTSEXAMPLE PLUGIN: SNP FINDER

Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

Power of visual analytics• task: find the correct parameter for some command line tool

Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

Plugin Framework• unlocks the potential for performing visual analytics

• platform is beneficial for both users and tool developers

for users: perform data analyses on-the-fly within a visual environment using the latest tools

for programmers: enables simple development and deployment of various programs

Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

Plugin Development• plugin development is easy• API contains over a hundred prebuilt functions (e.g. get

track data, add bookmarks, draw custom graphics, etc.)• SDK includes API and example plugin project on website

CONCLUSIONS

Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

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• novel features: e.g. table view, visualization modes,

data selection, 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/

Acknowledgements

Savant TeamMarc Fiume, Vanessa Williams, Andrew Brook, Michael Brudno

Usability and TestingPaul Medvedev, Misko Dzamba, Nilgun Donmez,

Daniel Lister, Andy Pang, Elango Cheran

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