Savant Genome Browser

SAVANT GENOME BROWSER

Marc FiumeDepartment of Computer ScienceUniversity of Toronto

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

High Throughput Sequencing• HTS machines can read billions of nucleotide bases per run• interpretation and analysis challenge• many separate tools for computational 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

• 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

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


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


Plugin API

Rangeget/set rangezoom in/outlisten for range change

Bookmarksadd / remove bookmark(s)navigate to bookmarkget bookmark(s)listen for bookmarks change

Tracksadd / remove track(s)get track data (in-range or whole genome)

change colour schemechange visualization mode

Otherget position of mouse on genomecapture screenshot

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

UIedit menus draw custom graphics


On-the-fly SNP Finder

listen for range change

get track data in range

DETECT 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

CONCLUSIONS & FUTURE WORK



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


Future work• external datasources • e.g. SQL database, 1000 Genomes Project Online DB

• improve and increase data format support• grow user and developer community


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


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

Documents

Transcript of Savant Genome Browser