Savant Genome Browser
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SAVANT GENOME BROWSER Marc Fiume Department of Computer Science University of Toronto
description
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. - PowerPoint PPT Presentation
Transcript of Savant Genome Browser
SAVANT GENOME BROWSERMarc FiumeDepartment of Computer ScienceUniversity 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 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 $$$ Y Y
Savant Genome Browser - http://compbio.cs.toronto.edu/savant/
• substantial disconnect between the processes of computational analysis and visualization
Tools for Genomic Data AnalysisTool Cost Computation Visualization
Read Alignment e.g. Bowtie, BWA
Free Y N
File Format Conversion e.g. Galaxy, SAMTools
Free Y N
Other Comand-line Toolse.g. Genetic Variation Discovery, Comparitive Genomics, etc.
Free Y N
UCSC Genome Browser Free N Y
Integrative Genomics Viewer Free N Y
GBrowse Free N Y
CLC Genomics Workbench $$$ Y Y
Savant Genome Browser Free Y Y
Savant Genome Browser - http://compbio.cs.toronto.edu/savant/
• 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 - http://compbio.cs.toronto.edu/savant/
Category Features
Data Formats FASTA, SAM/BAM, BED, WIG, GFF, tab-delimited
Speed and Efficiency Fast data accessScalable to very large input filesSmall memory footprint
Others Bookmarking favorite locationsTabular data viewLocking overview tracksNovel representation of paired-end reads makingstructural variations easy to identify
Operating Systems Works on Windows, Linux, and Mac
FEATURE DEMONSTRATION
Savant Genome Browser - http://compbio.cs.toronto.edu/savant/
INTERFACEHTS READ ALIGNMENTSEXAMPLE 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 - http://compbio.cs.toronto.edu/savant/
Plugin API
Savant Genome Browser - http://compbio.cs.toronto.edu/savant/
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 - http://compbio.cs.toronto.edu/savant/
listen for range change
get track data in range
DETECT SNPsDETECT 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 - 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 TeamMarc Fiume, Vanessa Williams, Andrew Brook,
Michael Brudno
Usability and TestingAlyssa 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 Main conference #J17Live demo on Sunday, 12:40 – 2:30
Website http://compbio.cs.toronto.edu/savantEmail [email protected]
Savant Genome Browser - http://compbio.cs.toronto.edu/savant/
