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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.

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savant genome browser

Savant Genome Browser

Marc Fiume

Department of Computer Science

University of Toronto

slide2
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/

slide3
Tools for Genomic Data Analysis
  • substantial disconnect between the processes of computational analysis and visualization

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

slide4
Tools for Genomic Data Analysis
  • substantial disconnect between the processes of computational analysis and visualization

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

slide5
Savant Genome Browser
  • platform for integratedvisual analysis of genomic data
    • feature-rich genome browser
    • computationally extensible via plugin framework

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

feature demonstration

FEATURE demonstration

  • INTERFACE
  • HTS READ ALIGNMENTS
  • EXAMPLE PLUGIN: SNP FINDER

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

slide7
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/

slide8
Plugin API
  • rich collection of functions to get data, perform computations, and create custom visualizations

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

slide9
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/

slide10
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

Conclusions & future work

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

slide12
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/

slide13
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/

slide14
Acknowledgements
  • Savant Team
  • Marc Fiume, Vanessa Williams, Andrew Brook,
  • Michael Brudno
  • Usability and Testing
  • Alyssa Rosenzweig, Mohit Jain, AkhilMathur,
  • Paul Medvedev, MiskoDzamba, NilgunDonmez,
  • Daniel Lister, Andy Pang, ElangoCheran

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

slide15
Try out Savant for yourself
  • Poster Main conference #J17
  • Live demo on Sunday, 12:40 – 2:30
  • Website http://compbio.cs.toronto.edu/savant
  • Email savant@cs.toronto.edu

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