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GfaViz: flexible and interactive visualization of GFA sequence graphs.

Giorgio Gonnella1, Niklas Niehus1, Stefan Kurtz1

  • 1Universität Hamburg, MIN-Fakultät, ZBH - Center for Bioinformatics, Hamburg, Germany.

Bioinformatics (Oxford, England)
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Summary

GfaViz is a new tool for visualizing sequence graphs in Graphical Fragment Assembly (GFA) formats. It supports GFA 2 features and allows customizable, exportable graph visualizations.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Graphical Fragment Assembly (GFA) formats are becoming standard for representing sequence graphs.
  • GFA 2 extends GFA 1, enabling representation of diverse graph types like scaffolding, variation, alignment, and metagenomic graphs.

Purpose of the Study:

  • To introduce GfaViz, an interactive graphical tool for visualizing sequence graphs in GFA format.
  • To support GFA 2 features and provide flexible visualization options.

Main Methods:

  • GfaViz offers interactive visualization of GFA sequence graphs.
  • Supports GFA 2 features with customizable layouts and styles.
  • Allows storing customizations within GFA tags and supports stylesheets.
  • Provides batch image generation via a command-line interface.

Main Results:

  • GfaViz effectively visualizes sequence graphs in GFA format, including GFA 2 features.
  • Users can customize visualizations with various layouts and styles.
  • Customizations are stored internally in GFA tags, eliminating external files.
  • Visualizations are exportable to raster and vector formats.

Conclusions:

  • GfaViz is a versatile tool for visualizing complex sequence graphs.
  • It enhances the utility of GFA 2 for diverse bioinformatics applications.
  • The tool facilitates clear and customizable representation of genomic data structures.