Interactive visualization of nanopore sequencing signal data with Squigualiser.

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.