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Updated: Jun 17, 2025

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Interactive visualization of nanopore sequencing signal data with Squigualiser.

Hiruna Samarakoon1,2,3, Kisaru Liyanage1,2,3, James M Ferguson2,3

  • 1School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia.

Bioinformatics (Oxford, England)
|August 13, 2024
PubMed
Summary

Squigualiser is a new toolkit for visualizing Nanopore sequencing signal data, enabling direct analysis of DNA/RNA modifications and structures. This open-source software offers an interactive browser for exploring complex raw signal data.

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Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Data Visualization

Background:

  • Nanopore sequencing generates large, complex raw signal data.
  • Direct analysis of this data can reveal DNA/RNA base modifications and secondary structures.
  • Current visualization strategies are insufficient for effective signal analysis and tool development.

Purpose of the Study:

  • To develop an intuitive and interactive toolkit for visualizing sequence-aligned Nanopore signal data.
  • To facilitate the exploration and analysis of raw signal data for identifying molecular features.
  • To support the development of new tools for Nanopore signal data analysis.

Main Methods:

  • Developed Squigualiser (Squiggle visualiser), an open-source software package.
  • Supports DNA and RNA sequencing data from Oxford Nanopore Technologies.
  • Compatible with various signal-alignment software, visualizing signal-to-read and signal-to-reference alignments at single-base resolution.
  • Generates an interactive HTML browser with customizable display options and a 'signal pileup' format for multiple reads.

Main Results:

  • Squigualiser provides intuitive, interactive visualization of sequence-aligned Nanopore signal data.
  • Enables single-base resolution viewing of both DNA and RNA sequencing data.
  • Integrates multiple reads into a 'signal pileup' and allows parallel display of different datasets.
  • Offers a unified platform purpose-built for raw signal data visualization.

Conclusions:

  • Squigualiser addresses the need for improved visualization strategies for Nanopore sequencing raw signal data.
  • It provides a powerful, user-friendly tool for researchers to explore and analyze complex signal data.
  • The open-source nature and broad compatibility of Squigualiser will benefit the wider scientific community.