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igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review.
James T Robinson1, Helga Thorvaldsdottir2, Jill P Mesirov1,3
1Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
igv-reports is a command-line tool that generates standalone HTML pages for interactive genomic data visualization. These reports embed read alignments and annotations, simplifying variant inspection without external file dependencies.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Variant inspection is crucial for genomic analysis.
- Existing tools may require complex setups or external data.
- Streamlining visualization workflows is essential for efficient research.
Purpose of the Study:
- To introduce igv-reports, a novel command-line tool.
- To enable the creation of self-contained HTML reports with interactive genomic visualizations.
- To facilitate variant inspection by embedding all necessary data and code.
Main Methods:
- Developed a command-line tool named igv-reports.
- Implemented functionality to generate standalone HTML pages.
- Integrated interactive visualization of read alignments and annotations.
Main Results:
- igv-reports successfully creates self-contained HTML reports.
- These reports embed interactive genomic visualizations.
- The generated reports require no external data file dependencies for visualization.
Conclusions:
- igv-reports simplifies the process of sharing and inspecting genomic variant data.
- The tool enhances variant inspection workflows by providing accessible, interactive reports.
- Standalone HTML reports improve data reproducibility and ease of use in genomics research.
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