NextBrowse: An integrated and interactive web-based genome browser for analyzing and interpreting genomic data

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Student
Whisenhunt, Phillip J
Degree
MS
Defense date
2012-04-23
Department
Computer Science
Commitee
Mittelman, David, Chair
Garner, Harold Ray, Member
Perez-Quinones, Manuel A., Member
Abstract
With the advent of high throughput sequencing technologies over the past decade there has been a surge in the amount of genomic data that needs to be analyzed and interpreted. Despite the availability of software frameworks such as the Genome Analysis Toolkit, data interpretation and analysis still requires human intervention and refinement. Genome browsers enable developers and users of sequence analysis tools to visualize, compare, and better interpret genomic data such as gene expression and functional annotations. We developed a next generation cross platform web-based genome browser, NextBrowse, for visualizing General Feature Format and Binary Alignment Map files. NextBrowse uses advanced visualization techniques such as 3D feature selection and transparency based on mapping quality, and improved Graphical User Interface elements such as individual track searching and textual and graphical reference location. NextBrowse is the first genome browser to allow BAM files to be streamed and visualized, the first genome browser to employ security measures, and the first to use only client side rendering. NextBrowse takes advantage of the open-source community, allowing developers and users to extend the project to fit their needs. NextBrowse along with all documentation is available for use at http://www.nextbrowse.vbi.vt.edu.
ETD Page
http://scholar.lib.vt.edu/theses/available/etd-04302012-125308/

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