UMIche: A UMI-centric analysis platform for enhancing molecular quantification accuracy in bulk and single-cell sequencing

UMIche: A UMI-centric analysis platform for enhancing molecular quantification accuracy in bulk and single-cell sequencing | 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 Research Article UMIche: A UMI-centric analysis platform for enhancing molecular quantification accuracy in bulk and single-cell sequencing Jianfeng Sun, Shuang Li, Stefan Canzar, Adam P. Cribbs This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6523497/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Unique molecular identifiers (UMIs) are widely utilised in RNA sequencing (RNA-seq) technologies to eliminate polymerase chain reaction (PCR) duplicates, thereby improving the accuracy of molecular quantification. However, synthesis errors in UMIs during sequencing often compromise the reliability of UMI counting. While various computational methods have been developed for error correction, the lack of a unified benchmarking and validation framework impedes systematic evaluation and optimisation. Here, we present UMIche, an open-source, UMI-centric computational platform designed to enhance UMI-assisted molecular quantification by offering a systematic, integrative, and extensible framework for UMI analysis. We show that through its integration of a broad spectrum of UMI collapsing methods and workflows, UMIche significantly advances the accuracy of molecular quantification and facilitates the generation of high-fidelity gene expression profiles. Molecular Biology Computational Biology Bioinformatics Biotechnology and Bioengineering Mathematical and Theoretical Biology Systems Biology Unique molecular identifiers (UMI) Molecular quantification Gene expression PCR duplicates Single-cell transcriptomics RNA-seq Full Text Additional Declarations The authors declare potential competing interests as follows: A.P.C is listed as an inventor on several patents filed by Oxford University Innovations concerning single-cell sequencing technologies. The other authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Supplementary Files SupplementaryInformation.docx Supplementary Information Cite Share Download PDF Status: Posted 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-6523497","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":450041821,"identity":"911f685d-ccce-434e-89f8-c364e57797a4","order_by":0,"name":"Jianfeng Sun","email":"data:image/png;base64,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","orcid":"https://orcid.org/0000-0002-1274-5080","institution":"Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford OX3 7LD, UK.","correspondingAuthor":true,"prefix":"","firstName":"Jianfeng","middleName":"","lastName":"Sun","suffix":""},{"id":450042297,"identity":"3abe2fc8-b435-41e0-9bbe-28753792795a","order_by":1,"name":"Shuang Li","email":"","orcid":"https://orcid.org/0009-0001-7932-9436","institution":"Gene Center, Ludwig-Maximilians University of Munich, Munich 81377, Germany","correspondingAuthor":false,"prefix":"","firstName":"Shuang","middleName":"","lastName":"Li","suffix":""},{"id":450042298,"identity":"262ba813-25b6-447c-8521-34de4ef2e38d","order_by":2,"name":"Stefan Canzar","email":"","orcid":"https://orcid.org/0000-0003-4719-8010","institution":"Faculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany","correspondingAuthor":false,"prefix":"","firstName":"Stefan","middleName":"","lastName":"Canzar","suffix":""},{"id":450042299,"identity":"65d02e08-055e-4941-9f05-885033437d9b","order_by":3,"name":"Adam P. 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