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BreakPoint Surveyor: a pipeline for structural variant visualization.
Matthew A Wyczalkowski1,2, Kristine M Wylie2,3, Song Cao1,2
1Oncology Division, Department of Medicine.
Bioinformatics (Oxford, England)
|June 6, 2017
Summary
BreakPoint Surveyor (BPS) is a new computational tool for identifying complex genomic rearrangements in DNA sequencing data. It aids in understanding structural variants by integrating multiple data types into a single visualization.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Complex genomic rearrangements, including viral integration, pose challenges in sequence data analysis.
- Accurate characterization of structural variants is crucial for understanding genetic diseases and biological processes.
Purpose of the Study:
- To introduce BreakPoint Surveyor (BPS), a novel computational pipeline.
- To enable the discovery, characterization, and visualization of complex genomic rearrangements.
- To facilitate the interpretation of structural variants in paired-end sequence data.
Main Methods:
- BPS is a computational pipeline implemented in R, Python, and BASH scripts.
- It analyzes paired-end sequence data to identify genomic rearrangements.
- The pipeline integrates breakpoint predictions, gene structure, read depth, and RNA-seq expression.
Main Results:
- BPS provides a comprehensive figure for interpreting structural variants.
- It successfully visualizes complex genomic events like viral genome integration.
- Facilitates the merging of diverse genomic and transcriptomic data.
Conclusions:
- BreakPoint Surveyor (BPS) is an effective tool for analyzing complex genomic rearrangements.
- It enhances the interpretation of structural variants through integrated visualization.
- BPS supports research in areas such as viral integration and genetic disease.
