biostudies-literatureUnknown8(1)Mak LComputational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architeNAR genomics and bioinformaticslqaf172https://www.ebi.ac.uk/biostudies/studies/S-EPMC12809600biostudies-literatureCAMP: a modular metagenomics analysis system for integrated multistep data exploration.PMC12809600Fuentes JJNakagawa MSeveryn JCSaito YPersaud SSchaaf SParas RKoag ERehrauer HWatanabe AJospin GLoubens MBorras SMoraes IOBurke CMPozdniakova SElaskandrany MForero JCPatrignani AFresia PWarashina TFelice SJinfessa ABecher KKhadka VSCarbajo MIii RAPNadalin FGreselle CHusser NPulatov BCoil DALewandowska DArevalo JEpping LRussell KGonnet GHSaito IJiminez EIwan ZPriya SFigueroa GSouza CHittle LESerpa MSLafontaine ICawthorne SToomey MLaine ESankar RWei WFarhat NOto YSato YCai XWDonahoe TRUrgiles CWong BMay MChiu SMcComb EToussaint NCArredondo FOrpilla JWong TOlmeda KPosada LZimmerman SBrion CMuscat MOliete JQVincent SHenry TSato SSato RKaur IKehdy FSGSuliman HBenchouaia MSato MMoreno MSato KOlawoyin RAKaur AMeng IChasapi AIDu SSilva JMNagy-Szakal DKahles ABode TMolina LFaiz IRuiz MSalas GAMOrtega MAlbuquerque GEChettouh ACiaramella KChen XChaker STaye MMelamed AInternational MetaSUB ConsortiumPugdeethosal PBitard-Feildel TChen MOta MSuganuma KTarcitano EGarcia MBoyd ARamcharan AMarinovic SAndrew WBoeri JThiebaut AFaure EGarcia LFeigin CMeoded RBolzli KGarcia CPardo-Este CIslam SRajendran KIslam RNasu MHoryslavets DPineda LGkotzis SSullivan JLiu TMunia MAndrade-Martinez JSBordigoni AAmorim MGLucaci AGCarbone AGuerra JSayara NPhillips AGalipon JHell ERoldan PCardenas ADavid LLeahy MMunoz CPerez MDa Silva OHazrin-Chong NHTomita MMason CEBriones ASantos PTSOluwadare TRamirez-Rojas AChem GBakhl KHernandez SMosella MSBaburyan SGhose SLMendez ASanchir KHess-Homeier DGregory TAngelov MKhavari MTomita IManoir DCastro ALannes RLiu EMKnights KHoxie INesimi AButtar ILiang WSalazar CAdel AHShiwa YAlexiev ASanchez JCastro SLago JHernandez PLWan AAsenjo FBello CPark YJArthur MGoldman SMoniruzzaman EEisen JABartelli TFAn NMaldonado DIshizuka SAlam IConte RMallari KGiovannelli DOunit RDarling AEOsuolale IOSchriml JRLitskevitch ABlyther BD'Alessandro BToscan RBPeros ABenitez DShakil MRivera MSomavilla NAOluwadare IAYemets OMohsin MThomas SChernomoretz AOteri FYeh GCCheung DMuner ONedunuri NRde Sousa NRWestfall DTong XKassim ASABlack CChatziefthimiou SFu CLemaire VDequeker CRivera AGeiger AEady NHomma CAraujo LFAly SPortilla MGPugh CESonohara YMeagher AMohan NIgarashi MNeff TDavidson NRLeong EDe Jong YTogashi TTogashi YOsma PSaravi ZOrdioni NBouly JPNavarrete IGNazario BTran JMRuiz SEBTurhan BNoushmehr HDayama GGiang DPPupiec ABertrand DYano HFrolova AWeekes SAventin NMoser JWGimenez MMamun MChen JWBreschi ACantillo AArnez LEAStark SGDas PHawkins-Zafarnia ABhattacharyya MThambiraja EJoo HWKumar SSQing TWieler LHTakahashi NDelmas SMeleshko DTakahashi KAranguren AGerner SMAquino CKim HJTierney BMuehlbauer ALAli KFonseca MASPathmanathan JSuarez-Villamil MAVelter FIvankovic TCentron DMiketic TLa Storia AKopbayeva MSmith RFoox JKhan SWilliams MHenriksen JRTakenaka IKWright RFerreira LPMalta TMKi MNg WCSperry JCarrillo KTerrero AMerino NCuebas DVivancos-Koopman RHuber MJames MTakahara FPatel SMoccia MDKuklin ABakere AMRobertiello ACasalot LBuczansla PHolik APiekar MAung TSLamba IBeurmann SDutan AVicedomini RO'Hara NBCedillo JKozhar MAuvinet JChrispin CHyland SIderzorig BYoshikawa SGonzalez JCastro AVBGonzalez ALin MSingh SKSasaki KSchinke AMVera-Wolf PSchori CIwashiro TChavan AKMozsary COuzounis CAJang SLivia MAFan LPrithiviraj BKoLoMonaco GKwong LKwong RBoifot KOHalary SRahiel SHoan NXJaubert MWunderlin TMendy IMOken GMarciniak NOsuolale OMLabaj PTsuda KGray AMenary WDezem FSCohen JFleiss APeters ARana STakagi SGithae DRead TDFlores DSegato FSetubal JCChaudhuri SRKubota NShari ACalderon DBenson JAfaq MBoldgiv BSabedot TSSluzek KKar SMoon SNoyvert ALi CFrancis ADorado SFauzi FObolenska MSuzuki CRojas NADorsey LVentorino VOrrego JAmran MACaballero HLo YHHartkopf FAmachee JBorrelli CMarques BBaudon FMoitra KArevalo HFVZafar LLeung MHYJackson SUsui MSan KMCastro AVMolinet JMiranda WMitsios APastuszek PVann LEChicas DMaruyama FZhang YHelfrich ERonkowski CBrindefalk BYeskova TBatdelger EMolomjamts OETymoshenko YPompa-Hogan BKajita TConger CWong YLTsurumaki TCossio CNGodoy LTruong CZhang SCifuentes EO'Brien KIqbal SBSepulveda FMiah KElhaik ECollin SToth OMahmoud SZhang ATang YMEttinger CLZheng YLakhneko OYamanaka RChan AHaehr WTomaselli AHassig Ade Lamotte GBurrell AMenon ATuz MJacobs JLisboa PMajid SAHajirasouliha INgwa EEscalera-Antezana JPVacant SNaveed HAlvarado-Arnez LEKrebs JDavenport LBNika ANoorzi HSiam RKim GCorsi FAyaz SLee LTang AAndrianjakarivony HBouchard SMiura RSupie AAMAl-Quaddoomi FSKobko-Litskevitch NLee HTanaka STassinari AAbdullah NRosario AAbraao MMatsuzaki YWerner JDias-Neto EBlanc GHastings JJASprinsky NBenoiston ASPriestman MChoudhry HKim SBonigk SHumphries EWolf SAJerier MLRahmatulloev SGonzalez-Poblete CMarchandon GNunes DNMangul SRatnanandan PLee YSimon GOsuolale YIto TLai TYSo EWang CIto SLysakova SDeng CKDevi MIto KDanko DChalangal JMignotte MPlaku AMatthys VKing RJMoldes MDahlhausen KESabina MYang JNarce AKantsypa VNakazawa NDesert AFlores JLVLu JAntelo VFriedman JRoth SShaaban HChavez FMathews NMustac TBynoe JValentine BBittner LMendez KNShirahata HMak LNosrati AFrench KBernardes JLaiola MShim HLosim STsonev SIPakrashi SNaeem ADe Sessions PFKato NRodo XSolano AHBHausler RMenor MRodriguez PMunim NNicolas ANicolas PQuiroga MPBenisty HIshikawa SAmpadu MMiyake KDe Lazzari EThomas AMNg SGuasco SMeydan CTakeda TNguyen GSchlapbach RArnan CRobinson CRicher RSchacher OShalaby SfalseCAMP: a modular metagenomics analysis system for integrated multistep data exploration.Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory archite2026-01-01T00:00:00Z2026 Mar2026-06-06T15:56:58.841Z2026-06-02T03:10:34.384ZS-EPMC128096004155193110.1093/nargab/lqaf172