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Brudno lab: A WHIRLWIND TOUR

Brudno lab: A WHIRLWIND TOUR. Marc Fiume Department of Computer Science University of Toronto. 1. what we do, our tools 2. Savant Genome Browser. Outline. WHAT WE DO. main focus: genomic analysis using output from high-throughput sequencing (HTS) machines

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Brudno lab: A WHIRLWIND TOUR

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  1. Brudno lab: A WHIRLWIND TOUR Marc Fiume Department of Computer Science University of Toronto

  2. 1. what we do, our tools • 2. Savant Genome Browser • Outline Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  3. WHAT WE DO Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  4. main focus: genomic analysis using output from high-throughput sequencing (HTS) machines • high throughput: sequence billions of nucleotides per week • poor data quality: “reads” are shorter; error profiles are poorly understood • What we do Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

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

  6. What to do with all these reads? Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  7. 1. Assembly • ASSEMBLY: • reconstruct the donor’s genome • “HapSembler”: specialized for highly polymorphic species Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  8. 2. Alignment • ALIGNMENT • find region in a “reference” genome that matches closely with each read; suggests similar origin from “donor” • “SHRiMP”:Short Read Mapping Package Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  9. 3. Genetic Variation Discovery • GENETIC VARIATION DISCOVERY • find differences between two genomes • between donor and reference • between two samples (e.g. tumour vs. normal) • “VARiD”, “MODiL”, and “CNVer” Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  10. Genetic Variation • Single Nucleotide Polymorphism (SNP): genomes have different nucleotides at corresponding positions • VARiD – VARiationIDentification • Insertions and Deletions (Indels): genomes have additional sequence put in or sequence taken out at corresponding locations • MODiL – Mixtures of Distributions Indel Locator • Copy Number Variation (CNV): genomes have a different number of the same sequence • CNVer Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  11. Our Bioinformatics Tools COMPRESSION ASSEMBLY (HapSembler) READ MAPPING (SHRiMP) VISUALIZATION (SAVANT) SNP DETECTION (VARiD) INDEL DETECTION (MODiL) CNV DETECTION (CNVer)

  12. SAVANT GENOME BROWSER Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  13. Genome Browsing, the old way Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  14. Challenge presented by HTS datasets • genomic data is generated in high volumes • HTS machines generate billions of bases per run • interpretation and analysis challenge • typical pipeline employs many separate tools for computation and visualization Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  15. Tools for HTS data analysis • substantial disconnect between the processes of computational analysis and visualization Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  16. Tools for Genomic Data Analysis • substantial disconnect between the processes of computational analysis and visualization Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  17. ASIDE: Cytoscape? • platform for visual analysis of networks • extensive plugin framework Bader Lab Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  18. 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/

  19. FEATURE demonstration • INTERFACE • HTS READ ALIGNMENTS • EXAMPLE PLUGIN: SNP FINDER Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  20. Power of visual analytics • task: find the correct parameter for command-line tool Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  21. Plugin Framework • unlocks the potential for performing visual analytics • beneficial for both users and tool developers • tool developers: simple platform for development and dissemination of work • plugindevelopment is easy • API contains over a hundred prebuilt functions (e.g. get track data, add bookmarks, draw custom graphics, etc.) Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

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

  23. 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/

  24. Acknowledgements Orion Vanessa Joe Nilgun Paul Vera Recep Andrew Vlad Mike Brudno Yue Marc Misko Yoni

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

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