IsoQuant: a tool for accurate novel isoform discovery with long reads

IsoQuant: a tool for accurate novel isoform discovery with long reads | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Brief Communication IsoQuant: a tool for accurate novel isoform discovery with long reads Andrey Prjibelski, Alla Mikheenko, Anoushka Joglekar, Alexander Smetanin, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-1571850/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 02 Jan, 2023 Read the published version in Nature Biotechnology → Version 1 posted You are reading this latest preprint version Abstract Long reads are reshaping RNA biology. However, determining alternative isoforms from long-read RNA data is a complex and incompletely solved problem even when the reference genome is known. Here we present IsoQuant - a reference-based tool that accurately discovers novel transcripts with at least 3-fold lower false positive rate and 1.8-fold increase in F1-score compared to other tools for Oxford Nanopore data. IsoQuant also increases performance for Pacific Biosciences data. Full Text Additional Declarations There is NO Competing Interest. Supplementary Files IsoQuantsupplementarymaterial.pdf Cite Share Download PDF Status: Published Journal Publication published 02 Jan, 2023 Read the published version in Nature Biotechnology → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-1571850","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Brief Communication","associatedPublications":[],"authors":[{"id":101104857,"identity":"6077ea9d-b853-4821-b70c-e42a21d4c007","order_by":0,"name":"Andrey Prjibelski","email":"","orcid":"","institution":"Saint Petersburg University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Andrey","middleName":"","lastName":"Prjibelski","suffix":""},{"id":101104858,"identity":"0ba5da82-602f-4cd7-9357-99bcaddc76af","order_by":1,"name":"Alla Mikheenko","email":"","orcid":"","institution":"Center for Algorithmic 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