VACmap: An Accurate Long-Read Aligner for Unraveling Complex Genomic Rearrangements

VACmap: An Accurate Long-Read Aligner for Unraveling Complex Genomic Rearrangements | 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 VACmap: An Accurate Long-Read Aligner for Unraveling Complex Genomic Rearrangements Shanfeng Zhu, Hongyu Ding, Fritz Sedlazeck, Christos Proukakis, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5088253/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 05 Jan, 2026 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Inversions, duplications, and other critical medically challenging variations are often ignored by routine genetic analyses. This is due to the complexity of these alleles but also because of the inability to accurately align them with state-of-the-art methods. We introduce VACmap, a novel non-linear long-read mapping method designed to improve detection of these difficult genomic regions, including critical genes like LPA and GBA1, which are significant risk factors for cardiovascular disease and Parkinson’s disease, respectively. Biological sciences/Computational biology and bioinformatics/Computational models Biological sciences/Computational biology and bioinformatics/Software Full Text Additional Declarations Yes there is potential Competing Interest. Fritz J Sedlazeck receives research support from Illumina, PacBio and Oxford Nanopore. The remaining authors declare no competing interests. Supplementary Files VACmapnrreportingsummary.pdf Reporting Summary VACmapnreditorialpolicychecklist.pdf Editorial Policy Checklist SupplementarydataVACmap09142024.docx Supplementary data Cite Share Download PDF Status: Published Journal Publication published 05 Jan, 2026 Read the published version in Nature Communications → 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-5088253","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Brief Communication","associatedPublications":[],"authors":[{"id":355644740,"identity":"c6c6d6ea-6a61-4538-b29b-d647f83b8441","order_by":0,"name":"Shanfeng 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