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TitleDevelopment of a prototype visualization approach for next-generation sequencing technologies using genome navigator framework
NameCui, Tiange (author), Grigoriev, Andrey (chair), Shain, Daniel H (internal member), Lee, Kwangwon (internal member), Rutgers University, Camden Graduate School,
Degree Date2012-05
Date Created2012
SubjectBiology,
Genomics,
Human gene mapping
DescriptionThe advent of next-generation sequencing (NGS) technologies has greatly accelerated the development of the genome analysis. Sequencing efficiency has improved significantly in last decade after the sequencing of the human genome was completed. A large number of NGS platforms have been developed with incredibly lower cost and higher throughputs. Terabyte of data are generated every day along with the NGS workstation, but the pace of analyzing these data is still not satisfactory. The lag between the available data and the interpretation tools will ultimately slow the progress of NGS. In this work, I aimed to add functionality to the display of NGS data in an existing genomic visualization tool - Genome Navigator (GN). By adding new features especially for the display of NGS data, the prototype GN can be used in various sequencing projects and help researchers visualize and interpret sequencing data, while exploring interested genomic region, and validating their hypotheses. After updates, the prototype GN is able to handle large amounts of sequencing data and display thousands of read at the same time. It supports several display modes such as stacked view, condensed view, and complex view. At different zoom levels, different amounts of details are shown to the users. Moreover, several utility tools have been developed to support GN when dealing with different input formats. Several new server interface features are designed for interaction with the user. I used the real sequencing data, tested the functionalities of the improvements, and had several positive results. I expect that GN will also be useful in other NGS applications and play an important role in today’s NGS research.
NoteM.S.
NoteIncludes bibliographical references
Noteby Tiange Cui
Genretheses
Persistent URLhttp://hdl.rutgers.edu/1782.1/rucore10005600001.ETD.000064968
Languageeng
CollectionCamden Graduate School Electronic Theses and Dissertations
Organization NameRutgers, The State University of New Jersey
RightsThe author owns the copyright to this work.