savant genome browser marc fiume department of computer science university of toronto

SAVANT GENOME BROWSER

Marc 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


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


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• platform for integrated visual analysis of genomic data• feature-rich genome browser• computationally extensible via plugin framework


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


INTERFACEHTS READ ALIGNMENTSEXAMPLE PLUGIN: SNP FINDER


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


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


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



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


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

savant genome browser marc fiume department of computer science university of toronto

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