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