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Assembly Graph Browser: interactive visualization of assembly graphs.

Alla Mikheenko1, Mikhail Kolmogorov2

  • 1Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia.

Bioinformatics (Oxford, England)
|February 5, 2019
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Summary
This summary is machine-generated.

We developed the Assembly Graph Browser (AGB), a tool for visualizing large genome assembly graphs. AGB offers novel functions for repeat analysis and graph contraction, improving genome assembly visualization.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome assembly projects traditionally focus on contigs and scaffolds.
  • Assembly graphs offer a more comprehensive representation of genomic data.
  • Interactive visualization of large assembly graphs presents significant computational challenges.

Purpose of the Study:

  • To develop a novel tool for visualizing large genome assembly graphs.
  • To extend existing visualization functionalities for complex genomic data.
  • To address the open problem of interactive visualization for large assembly graphs.

Main Methods:

  • Development of the Assembly Graph Browser (AGB) software tool.
  • Implementation of novel visualization techniques for large graphs.
  • Inclusion of functions for repeat analysis and graph contraction.

Main Results:

  • The Assembly Graph Browser (AGB) effectively visualizes large assembly graphs.
  • AGB incorporates new functionalities, including repeat analysis and graph contraction.
  • The tool enhances the interactive exploration of complex genome assemblies.

Conclusions:

  • The Assembly Graph Browser (AGB) provides an advanced solution for visualizing large genome assembly graphs.
  • AGB's novel features improve the analysis and interpretation of genomic assembly data.
  • This tool advances the field of genome assembly visualization and analysis.