Abstract
BackgroundNext generation sequencing (NGS) data treatment often requires mapping sequenced reads onto a reference genome for further analysis. Mapped data are commonly visualized using genome browsers. However, such software are not suited for a publication-ready and versatile representation of NGS data coverage, especially when multiple experiments are simultaneously treated.ResultsWe developed ‘VING’, a stand-alone R script that takes as input NGS mapping files and genome annotations to produce accurate snapshots of the NGS coverage signal for any specified genomic region. VING offers multiple viewing options, including strand-specific views and a special heatmap mode for representing multiple experiments in a single figure.ConclusionsVING produces high-quality figures for NGS data representation in a genome region of interest. It is available at http://vm-gb.curie.fr/ving/. We also developed a Galaxy wrapper, available in the Galaxy tool shed with installation and usage instructions.
Highlights
Generation sequencing (NGS) data treatment often requires mapping sequenced reads onto a reference genome for further analysis
Annotation files are read by a custom function that only loads genomic features within coordinates defined by the users, enabling a faster operation
The signal is plotted in a strandspecific manner using any of the three visualization modes: “classic” coverage plots using solid areas; “line” plots using lines of different colors and/or styles; “heatmap” views based on a color-code to reveal high/low-density coverage regions
Summary
We developed ‘VING’, a stand-alone R script that takes as input NGS mapping files and genome annotations to produce accurate snapshots of the NGS coverage signal for any specified genomic region. VING offers multiple viewing options, including strand-specific views and a special heatmap mode for representing multiple experiments in a single figure
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