Interactive visualisation of raw nanopore signal data with Squigualiser

Nanopore sequencing measures ionic current during the translocation of DNA, RNA or protein molecules through a nanoscale protein pore. This raw current signal data can be 'basecalled' into sequence information and has the potential to identify other diverse molecular features, such as base modifications, secondary structures, etc. Despite the unique properties and potential utility of nanopore signal data, there are currently limited options available for signal data visualisation. To address this, we have developed Squigualiser, a toolkit for intuitive, interactive visualisation of sequence-aligned signal data, which currently supports both DNA and RNA sequencing data from Oxford Nanopore Technologies (ONT) instruments. A series of methodological innovations enable efficient alignment of raw signal data to a reference genome/transcriptome with single-base resolution. Squigualiser generates an interactive signal browser view (HTML file), in which the user can navigate across a genome/transcriptome region and customise the display. Multiple independent reads are integrated into a signal 'pileup' format and different datasets can be displayed as parallel tracks to facilitate their comparison. Squigualiser provides the most sophisticated framework for nanopore signal data visualisation to date and will catalyse new advances in signal analysis. We provide Squigualiser as an open-source tool for the nanopore community: https://github.com/hiruna72/squigualiser ### Competing Interest Statement I.W.D. manages a fee-for-service sequencing facility at the Garvan Institute of Medical Research and is a customer of Oxford Nanopore Technologies but has no further financial relationship. H.G., J.M.F. and I.W.D. have previously received travel and accommodation expenses from Oxford Nanopore Technologies. The authors declare no other competing financial or non-financial interests.