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Updated: Feb 28, 2026

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runBNG: a software package for BioNano genomic analysis on the command line.

Yuxuan Yuan1, Philipp E Bayer1, Huey-Tyng Lee1,2

  • 1School of Biological Sciences, University of Western Australia, Perth, WA, Australia.

Bioinformatics (Oxford, England)
|June 13, 2017
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Summary

We developed runBNG, an open-source software package for command-line genomic analysis. This tool simplifies complex BioNano genomic analyses, offering high customizability and a unified platform for tasks like de novo assembly and structural variation detection.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Genomic analysis often involves complex, multi-step pipelines.
  • Existing software may lack integration and customizability.

Purpose of the Study:

  • To develop an integrated, user-friendly software package for BioNano genomic analysis.
  • To streamline common genomic analysis workflows.

Main Methods:

  • Developed runBNG, an open-source bash script.
  • Integrated BioNano genomic analysis tools into a single command-line script.
  • Requires BioNano IrysSolve packages, GCC, Perl, and Python.

Main Results:

  • runBNG enables quality control of single-molecule maps.
  • Facilitates optical map de novo assembly and inter-map comparisons.
  • Supports super-scaffolding and structural variation detection.

Conclusions:

  • runBNG offers a unified platform for BioNano genomic analyses.
  • Provides high customizability compared to existing tools like BioNano IrysView and KSU scripts.
  • Enhances efficiency and accessibility of complex genomic analyses.