Afanc: a Metagenomics Tool for Variant Level Disambiguation of NGS Datasets

Afanc: a Metagenomics Tool for Variant Level Disambiguation of NGS Datasets | 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 Article Afanc: a Metagenomics Tool for Variant Level Disambiguation of NGS Datasets Arthur Morris, Anna Price, Thomas Connor This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3413631/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 Genomics is amongst the most powerful tools available for mounting a clinical response to infectious disease. The accurate and precise taxonomic evaluation of pathogens is essential when building a picture of pathogenicity, virulence, transmission, and drug resistance. Carrying out such profiling in a high throughput manner necessitates the development of reliable bioinformatic tools. Here we present Afanc, a novel metagenomic profiler which is sensitive down to species and strain level taxa, and capable of elucidating the complex pathogen profile of compound datasets. We compared Afanc against currently available cutting edge profilers using 3 datasets: single species read sets simulated from the full Mycobacteriaceae taxonomic landscape; compound read sets containing multiple Mycobacteriaceae species and variants; and real data covering the majority of the M. tuberculosis lineage taxonomic space. Afanc outperformed all profilers, both generic and Mycobacteriaceae specific, across all tested fields. As a species agnostic profiler, we predict that Afanc will be of great utility when carrying out highly specific and sensitive pathogen profiling of clinical datasets. Such analyses are essential in advising both the clinical response to an individual disease case, and in forming the foundation of epidemiological surveys. Biological sciences/Computational biology and bioinformatics/Classification and taxonomy Biological sciences/Microbiology/Infectious-disease diagnostics Full Text Additional Declarations There is NO Competing Interest. 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. 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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-3413631","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":460501712,"identity":"3a2802a1-ebf9-41a2-8cc7-b3be8fd0e855","order_by":0,"name":"Arthur Morris","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA5klEQVRIiWNgGAWjYHACNjjrAEMFkGRmbiCggxlZyxmQACMJWhgY28Akfi38s88fe8y753A0v/TZhwd/zquN5m8HavlRsQ2nFolzyezGPM8O587sSzc4zLvteO6Mw4wNjD1nbuO25gwzmzTPgbTcDWfYGA4zbjuW2wDUwszYhluLPLKWgz/nHMudT0iLAUSLDVjLAd6GmtwNhLQYnmE2k5wD1DKzB+gwnmMHcjcCtRzE5xe5M4zPJN4ckMjt52Fj/vijpi533vnDBx/8qMDjfTRwGEweIFo9ENSRongUjIJRMApGCAAABnxZTVt5jMgAAAAASUVORK5CYII=","orcid":"https://orcid.org/0009-0004-6579-0418","institution":"Cardiff University","correspondingAuthor":true,"prefix":"","firstName":"Arthur","middleName":"","lastName":"Morris","suffix":""},{"id":460501713,"identity":"fa3b145e-ec9a-418a-96a2-8bca332b747a","order_by":1,"name":"Anna Price","email":"","orcid":"","institution":"Cardiff University","correspondingAuthor":false,"prefix":"","firstName":"Anna","middleName":"","lastName":"Price","suffix":""},{"id":460501714,"identity":"e16d0442-28c5-4013-8ef3-0eaffe817066","order_by":2,"name":"Thomas Connor","email":"","orcid":"","institution":"Cardiff University","correspondingAuthor":false,"prefix":"","firstName":"Thomas","middleName":"","lastName":"Connor","suffix":""}],"badges":[],"createdAt":"2023-10-05 14:26:16","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3413631/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3413631/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":83427653,"identity":"ac0f5167-7dbf-4ea8-8989-c75236e09453","added_by":"auto","created_at":"2025-05-26 05:41:44","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":816234,"visible":true,"origin":"","legend":"","description":"","filename":"Afancmanuscriptnature.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3413631/v1_covered_dbc3003a-c67e-4d38-a76f-c340858f8f6b.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Afanc: a Metagenomics Tool for Variant Level Disambiguation of NGS Datasets","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":"","lastPublishedDoi":"10.21203/rs.3.rs-3413631/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3413631/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Genomics is amongst the most powerful tools available for mounting a clinical response to infectious disease. 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