Squigualiser

Squigualiser visualises sequence-aligned raw nanopore signal data with single-base resolution for DNA and RNA sequencing data from Oxford Nanopore Technologies instruments.

Key Features:

• Signal Alignment: Efficiently aligns raw signal data to a reference genome or transcriptome with single-base resolution.
• Interactive Signal Browser: Generates an interactive HTML-based signal browser view for navigating across genome or transcriptome regions with customisable display.
• Signal Pileup: Integrates multiple independent reads into a signal pileup format for visualising aligned signal data.
• Parallel Track Comparison: Displays different datasets as parallel tracks to facilitate comparison between samples or conditions.

Scientific Applications:

• Base Modification Detection: Supports visual analysis of raw current signal data to identify base modifications and other molecular features beyond primary sequence.
• Secondary Structure Analysis: Enables investigation of RNA secondary structures and other diverse molecular features through raw signal visualisation.
• DNA and RNA Sequencing Analysis: Facilitates intuitive analysis of both DNA and RNA nanopore sequencing data through interactive signal alignment and visualisation.

Methodology:

Squigualiser employs methodological innovations for efficient alignment of raw signal data to a reference genome or transcriptome with single-base resolution, generating interactive HTML visualisations including signal browser views and pileup plots.