Check My Sample Sheet: a Web Application for Validating Illumina Sample Sheets Before Demultiplexing

Check My Sample Sheet: a Web Application for Validating Illumina Sample Sheets Before Demultiplexing | 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 Check My Sample Sheet: a Web Application for Validating Illumina Sample Sheets Before Demultiplexing Laure Lemée, Rania Ouazahrou, Etienne Kornobis, Thomas Cokelaer This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5268893/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 The proper configuration of an Illumina sequencing run is paramount to its success, and the sample sheet, which summarizes sample metadata, is a critical component. To ensure accurate demultiplexing and downstream analysis, validation of this sample sheet is essential. Here, we present a user-friendly web application built with Streamlit, leveraging the IEM Python module from the Sequana Python library, designed for thorough sanity checks of Illumina sample sheets. Our application offers a streamlined solution for sequencing platforms seeking to validate sample sheets prior to initiating demultiplexing processes. Through an intuitive interface, users can easily upload sample sheet files, triggering a suite of validation checks that include crucial parameters such as sample duplication, consistency, and adherence to Illumina formatting standards. The Web application Check My Sample Sheet empowers users to identify and rectify potential problems preemptively, mitigate errors, and optimize sequencing outcomes. Furthermore, our application's open-source nature facilitates extensibility, allowing for customization to specific workflow requirements or other types of sample sheet formats. Bioinformatics NGS demultiplexing web application Full Text Additional Declarations The authors declare no competing interests. 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-5268893","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":366310934,"identity":"47972ce7-06d2-40bd-81a6-10f7bdcfa93d","order_by":0,"name":"Laure Lemée","email":"","orcid":"","institution":"Institut Pasteur","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Laure","middleName":"","lastName":"Lemée","suffix":""},{"id":366310935,"identity":"54e731c7-3927-438a-9fb6-67bd27bee9cf","order_by":1,"name":"Rania Ouazahrou","email":"","orcid":"","institution":"Institut Pasteur","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Rania","middleName":"","lastName":"Ouazahrou","suffix":""},{"id":366310936,"identity":"036c8311-fd62-492e-9f05-4f24c84550f3","order_by":2,"name":"Etienne Kornobis","email":"","orcid":"","institution":"Institut Pasteur","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Etienne","middleName":"","lastName":"Kornobis","suffix":""},{"id":366310937,"identity":"80b70a72-314d-4214-bedf-e102486ec640","order_by":3,"name":"Thomas Cokelaer","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABFElEQVRIiWNgGAWjYDACCRiDh4HxAJCSg8uwN2DXwYOkhQGkxRiIGcGKeQ4QqSWxgZAWe+nmoxt+/GGQ5+c5fODAj4p76dvZjz9/8LHtHgOPNHY9PDLH0m72tjEYzuxtSzjYc6Y4d2dPjmHjzLZiBh6+BBwOyzG7wdvAkGBwnsfgAG9bQu6GAzmMzUAGgz0PLr/kmN388wekhf/Dwb//EtINzj9/2PwXqIUHj5bbPGxALWd7GA7zNiQkGNxIMGxmxKflRlrabdk2CcOZPccMDsscSzDcOeMNkHMugQeXFvYZycduvvljAwyx5IcP39QkyJvzpz/48KMsQQ6XFiiQQDANYPbj1YACDAgrGQWjYBSMghEGAH2OX8O/IpBVAAAAAElFTkSuQmCC","orcid":"","institution":"Institut Pasteur","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Thomas","middleName":"","lastName":"Cokelaer","suffix":""}],"badges":[],"createdAt":"2024-10-15 12:54:06","currentVersionCode":1,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false,"coiExplicitlySet":false},"doi":"10.21203/rs.3.rs-5268893/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5268893/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":66739674,"identity":"b6fdcf8a-03f3-43af-b702-4fbb0296ae23","added_by":"auto","created_at":"2024-10-16 05:38:03","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":516549,"visible":true,"origin":"","legend":"","description":"","filename":"checksamplesheetpreprint.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5268893/v1_covered_8b348844-c514-432c-9783-9af6164fe319.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eCheck My Sample Sheet: a Web Application for Validating Illumina Sample Sheets Before Demultiplexing\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"NGS, demultiplexing, web application","lastPublishedDoi":"10.21203/rs.3.rs-5268893/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5268893/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cbr\u003e\u003c/p\u003e\n\u003cp\u003eThe proper configuration of an Illumina sequencing run is paramount to its success, and the sample sheet, which summarizes sample metadata, is a critical component. 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