{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T15:28:34Z","timestamp":1768922914506,"version":"3.49.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,8,13]],"date-time":"2024-08-13T00:00:00Z","timestamp":1723507200000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Australian Medical Research Futures Fund","award":["MRF1173594"],"award-info":[{"award-number":["MRF1173594"]}]},{"name":"Australian Medical Research Futures Fund","award":["MRF2023126"],"award-info":[{"award-number":["MRF2023126"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Nanopore sequencing current signal data can be \u2018basecalled\u2019 into sequence information or analysed directly, with the capacity to identify diverse molecular features, such as DNA\/RNA base modifications and secondary structures. However, raw signal data is large and complex, and there is a need for improved visualization strategies to facilitate signal analysis, exploration and tool development.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Squigualiser (Squiggle visualiser) is a toolkit for intuitive, interactive visualization of sequence-aligned signal data, which currently supports both DNA and RNA sequencing data from Oxford Nanopore Technologies instruments. Squigualiser is compatible with a wide range of alternative signal-alignment software packages and enables visualization of both signal-to-read and signal-to-reference aligned data at single-base resolution. Squigualiser generates an interactive signal browser view (HTML file), in which the user can navigate across a genome\/transcriptome region and customize the display. Multiple independent reads are integrated into a \u2018signal pileup\u2019 format and different datasets can be displayed as parallel tracks. Although other methods exist, Squigualiser provides the community with a software package purpose-built for raw signal data visualization, incorporating a range of new and existing features into a unified platform.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Squigualiser is an open-source package under an MIT licence: https:\/\/github.com\/hiruna72\/squigualiser. The software was developed using Python 3.8 and can be installed with pip or bioconda or executed directly using prebuilt binaries provided with each release.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae501","type":"journal-article","created":{"date-parts":[[2024,8,13]],"date-time":"2024-08-13T18:28:44Z","timestamp":1723573724000},"source":"Crossref","is-referenced-by-count":10,"title":["Interactive visualization of nanopore sequencing signal data with <i>Squigualiser<\/i>"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5812-1046","authenticated-orcid":false,"given":"Hiruna","family":"Samarakoon","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, University of New South Wales , Sydney, NSW 2052,","place":["Australia"]},{"name":"Genomics and Inherited Disease Program, Garvan Institute of Medical Research , Sydney, NSW 2010,","place":["Australia"]},{"name":"Centre for Population 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