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ASCIIGenome: a command line genome browser for console terminals.

Dario Beraldi1

  • 1Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK.

Bioinformatics (Oxford, England)
|January 26, 2017
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Summary
This summary is machine-generated.

ASCIIGenome is a novel command-line genome browser that displays genomic data directly in terminal windows. This tool facilitates script integration and batch processing, overcoming limitations of graphical user interfaces for efficient data exploration.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Traditional genome browsers rely on graphical user interfaces (GUIs).
  • GUIs present challenges for scripting and automated data analysis.
  • There is a need for terminal-based tools for genomic data exploration.

Purpose of the Study:

  • Introduce ASCIIGenome, a command-line interface (CLI) genome browser.
  • Enable seamless integration of genomic data visualization into command-line workflows.
  • Facilitate efficient data exploration and analysis through scripting.

Main Methods:

  • ASCIIGnome is developed in Java, ensuring cross-platform compatibility.
  • The tool supports common genomic data types and remote data access via FTP.
  • Performance in terms of speed and memory usage is competitive with existing browsers.

Main Results:

  • ASCIIGenome provides direct genomic data visualization within terminal windows.
  • The CLI design allows for easy integration with shell scripts and batch processing.
  • It offers a viable alternative for users preferring command-line operations.

Conclusions:

  • ASCIIGenome overcomes GUI limitations by operating exclusively via CLI.
  • It enables streamlined genomic data exploration and integration into computational pipelines.
  • The tool enhances the efficiency of analyzing large genomic datasets.