BioChef: A Client-Side WebAssembly-Based Workflow Builder for Genomic Data Analysis

BioChef: A Client-Side WebAssembly-Based Workflow Builder for Genomic Data Analysis | 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 software BioChef: A Client-Side WebAssembly-Based Workflow Builder for Genomic Data Analysis Joaquim Rosa, Jorge Miguel Silva, José Luis Oliveira This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7697498/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 09 Apr, 2026 Read the published version in BMC Bioinformatics → Version 1 posted 11 You are reading this latest preprint version Abstract Background: Genomics analyses often rely on command-line tools executed via remote servers, imposing usability barriers for non-technical users and raising privacy concerns. WebAssembly (WASM) enables native-code execution directly in web browsers, eliminating installations and data transfers. Results: We introduce BioChef, a client-side genomic workflow platform that uses WASM. BioChef compiles a genomics toolkit into browser-executable modules accessible via an intuitive drag-and-drop GUI. The system provides real-time validation, flexible input methods (form-based and JSON), intermediate step inspections, and reproducible workflows exportable as bash scripts or configuration files. Performance benchmarks across major browsers (Chromium, Gecko, WebKit) demonstrate rapid initialization (LCP 0.583 s), responsive interactivity (INP 30.5 ms), minimal layout shifts (CLS 0.01), and acceptable overhead (average 181.5 ms initial WASM module load). Although browser execution introduced performance penalties (~130x slower than native), BioChef workflows still significantly outperformed traditional web services such as Galaxy by avoiding network delays and server-side queueing (11.3x faster in a standard pipeline benchmark). Conclusions: BioChef shows how WebAssembly on the client side can democratize genomic data processing, ensuring privacy, reproducibility and ease of use without external dependencies. To our knowledge, this is the first fully client-side, graphical genomic workflow environment powered by WASM. Availability: Online demo: https://ieeta-pt.github.io/Biochef . Source code, WebAssembly binaries, and reproducibility artifacts: https://github.com/ieeta-pt/Biochef . WebAssembly Bioinformatics Workflows Web-Based Applications Workflow Management Systems Human-Computer Interaction Genomic Data Processing Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Published Journal Publication published 09 Apr, 2026 Read the published version in BMC Bioinformatics → Version 1 posted Editorial decision: Revision requested 19 Jan, 2026 Reviews received at journal 16 Jan, 2026 Reviewers agreed at journal 16 Dec, 2025 Reviews received at journal 27 Oct, 2025 Reviewers agreed at journal 23 Oct, 2025 Reviewers agreed at journal 09 Oct, 2025 Reviewers invited by journal 09 Oct, 2025 Editor assigned by journal 08 Oct, 2025 Editor invited by journal 06 Oct, 2025 Submission checks completed at journal 04 Oct, 2025 First submitted to journal 04 Oct, 2025 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. 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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-7697498","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"software","associatedPublications":[],"authors":[{"id":532364935,"identity":"5bccbf77-cab2-4961-a3ed-0dddc45d3030","order_by":0,"name":"Joaquim Rosa","email":"","orcid":"","institution":"University of Aveiro","correspondingAuthor":false,"prefix":"","firstName":"Joaquim","middleName":"","lastName":"Rosa","suffix":""},{"id":532364936,"identity":"2bda8a20-cd63-47ca-90a1-16ba1243fbda","order_by":1,"name":"Jorge Miguel Silva","email":"data:image/png;base64,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","orcid":"","institution":"University of Aveiro","correspondingAuthor":true,"prefix":"","firstName":"Jorge","middleName":"Miguel","lastName":"Silva","suffix":""},{"id":532364937,"identity":"7e8f3854-400b-4a87-9497-9c8153d46740","order_by":2,"name":"José Luis Oliveira","email":"","orcid":"","institution":"University of Aveiro","correspondingAuthor":false,"prefix":"","firstName":"José","middleName":"Luis","lastName":"Oliveira","suffix":""}],"badges":[],"createdAt":"2025-09-23 20:08:21","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7697498/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7697498/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12859-026-06431-1","type":"published","date":"2026-04-09T15:57:16+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":94148062,"identity":"6c157c03-1ccd-41f4-8d40-468afe1fe1f6","added_by":"auto","created_at":"2025-10-22 23:08:32","extension":"json","order_by":0,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":5334,"visible":true,"origin":"","legend":"","description":"","filename":"e80289ba26e2400fb39bc52b636c572e.json","url":"https://assets-eu.researchsquare.com/files/rs-7697498/v1/96befc9eefa904466f37391d.json"},{"id":106809700,"identity":"a1c45f0d-bc28-481a-8f00-cb536e244b29","added_by":"auto","created_at":"2026-04-13 16:12:15","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1887341,"visible":true,"origin":"","legend":"","description":"","filename":"Biochef.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7697498/v1_covered_7c29bf0b-ab63-4750-b506-5905cabae118.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"BioChef: A Client-Side WebAssembly-Based Workflow Builder for Genomic Data Analysis","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-bioinformatics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"binf","sideBox":"Learn more about [BMC Bioinformatics](http://bmcbioinformatics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/binf","title":"BMC Bioinformatics","twitterHandle":"@BMC_Bioinformatics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"WebAssembly, Bioinformatics Workflows, Web-Based Applications, Workflow Management Systems, Human-Computer Interaction, Genomic Data Processing","lastPublishedDoi":"10.21203/rs.3.rs-7697498/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7697498/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Background: Genomics analyses often rely on command-line tools executed via remote servers, imposing usability barriers for non-technical users and raising privacy concerns. 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