D2Sim: A computational simulator for nanopore sequencing based DNA data storage

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dc.contributor.authorSankar, Subhasiny
dc.contributor.authorYixin, Wang
dc.contributor.authorNoor-A-Rahim, Md
dc.contributor.authorGunawan, Erry
dc.contributor.authorGuan, Yong Liang
dc.contributor.authorPoh, Chueh Loo
dc.date.accessioned2026-09-07T14:59:01Z
dc.date.available2026-09-07T14:59:01Z
dc.date.issued2026-07-23
dc.description.abstractDNA data storage has gained significant attention because of its high storage density and durability. However, errors during the storage and reading processes compromise data integrity, prompting research into error correction strategies. Researchers have explored physical (data copies) and logical redundancy (added redundancy in error-correcting codes) to mitigate errors. Evaluating these designs and reconstruction methods typically involves time-consuming and costly trials. To streamline this process, we designed a computational channel simulator, namely D2Sim, for Nanopore sequencing-based DNA data storage. This simulator mimics real experiments, generating data with certain redundancy and errors at the receiver. Integrated with DeepSimulator, D2Sim outputs signals closely resembling actual signals of Nanopore-based DNA storage. Comparative analysis reveals that the proposed simulator yields 16.7% to 88.7% lower sample difference deviations than signals from DeepSimulator alone. This cost-effective and time-efficient tool facilitates the assessment of physical and logical redundancy for data reconstruction in DNA data storage without the need for real-time experiments.en
dc.description.versionAccepted Version
dc.format.extent12
dc.format.mimetypeapplication/pdfen
dc.identifier.authororcidSankar, Subhasiny
dc.identifier.authororcidYixin, Wang
dc.identifier.authororcidNoor-A-Rahim, Md§0000-0003-0587-3145
dc.identifier.authororcidGunawan, Erry
dc.identifier.authororcidGuan, Yong Liang
dc.identifier.authororcidPoh, Chueh Loo
dc.identifier.citationSankar, S, Yixin, W, Noor-A-Rahim, M, Gunawan, E, Guan, Y L & Poh, C L 2026, 'D2Sim: A computational simulator for nanopore sequencing based DNA data storage', IEEE Transactions on Computational Biology and Bioinformatics, pp. 1-12. https://doi.org/10.1109/TCBBIO.2026.3716589
dc.identifier.doi10.1109/TCBBIO.2026.3716589
dc.identifier.endpage12
dc.identifier.issn2998-4165
dc.identifier.journaltitleIEEE Transactions on Computational Biology and Bioinformatics
dc.identifier.otherORCID: /0000-0003-0587-3145/work/226051295
dc.identifier.startpage1
dc.identifier.urihttps://hdl.handle.net/10468/19182
dc.language.isoen
dc.publisherInstitute of Electrical and Electronics Engineers Inc.
dc.relation.urihttps://www.scopus.com/pages/publications/105045760420
dc.rights© 2026, IEEE. For the purpose of open availability, the author has applied a public copyright licence to the Author Accepted Manuscript arising from this submission to enable immediate repository dissemination.
dc.rights.accessrightsopen access
dc.rights.licensenameAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.statusPeer reviewed
dc.subjectBioinformatic tool
dc.subjectBiomolecular errors
dc.subjectComputational simulator
dc.subjectDNA data storage
dc.subjectLogical and sequencing redundancy
dc.subjectRandom process
dc.subject[ComputerScience]
dc.titleD2Sim: A computational simulator for nanopore sequencing based DNA data storageen
dc.typeArticle (peer-reviewed)
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