{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T05:49:52Z","timestamp":1789192192977,"version":"build-2803163510"},"reference-count":69,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T00:00:00Z","timestamp":1763424000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003163","name":"Forschungszentrum J\u00fclich","doi-asserted-by":"publisher","award":["NBI-014"],"award-info":[{"award-number":["NBI-014"]}],"id":[{"id":"10.13039\/501100003163","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003163","name":"Forschungszentrum J\u00fclich","doi-asserted-by":"publisher","award":["NBI-022"],"award-info":[{"award-number":["NBI-022"]}],"id":[{"id":"10.13039\/501100003163","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003163","name":"Forschungszentrum J\u00fclich","doi-asserted-by":"publisher","award":["NBI-004"],"award-info":[{"award-number":["NBI-004"]}],"id":[{"id":"10.13039\/501100003163","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003163","name":"Forschungszentrum J\u00fclich","doi-asserted-by":"publisher","award":["NBI-008"],"award-info":[{"award-number":["NBI-008"]}],"id":[{"id":"10.13039\/501100003163","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003163","name":"Forschungszentrum J\u00fclich","doi-asserted-by":"publisher","award":["NBI-013"],"award-info":[{"award-number":["NBI-013"]}],"id":[{"id":"10.13039\/501100003163","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003163","name":"Forschungszentrum J\u00fclich","doi-asserted-by":"publisher","award":["NBI-010"],"award-info":[{"award-number":["NBI-010"]}],"id":[{"id":"10.13039\/501100003163","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003163","name":"Forschungszentrum J\u00fclich","doi-asserted-by":"publisher","award":["NBI-016"],"award-info":[{"award-number":["NBI-016"]}],"id":[{"id":"10.13039\/501100003163","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003163","name":"Forschungszentrum J\u00fclich","doi-asserted-by":"publisher","award":["NBI-001"],"award-info":[{"award-number":["NBI-001"]}],"id":[{"id":"10.13039\/501100003163","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF21SA0072700"],"award-info":[{"award-number":["NNF21SA0072700"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005156","name":"Alexander von Humboldt Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005156","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["EXC 2124\\u2013390838134"],"award-info":[{"award-number":["EXC 2124\\u2013390838134"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["455787709"],"award-info":[{"award-number":["455787709"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018929","name":"German Network for Bioinformatics Infrastructure","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100018929","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002345","name":"Eberhard Karls Universit\u00e4t T\u00fcbingen","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002345","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports Methods"],"published-print":{"date-parts":[[2026,1]]},"DOI":"10.1016\/j.crmeth.2025.101266","type":"journal-article","created":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T15:42:21Z","timestamp":1766504541000},"page":"101266","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"title":["MMonitor for real-time monitoring of microbial communities using long reads"],"prefix":"10.1016","volume":"6","author":[{"given":"Timo N.","family":"Lucas","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulrike","family":"Biehain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anupam","family":"Gautam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kurt","family":"Gemeinhardt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias","family":"Lass","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Konzalla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth E.","family":"Ley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Largus T.","family":"Angenent","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2961-604X","authenticated-orcid":false,"given":"Daniel H.","family":"Huson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.crmeth.2025.101266_bib1","doi-asserted-by":"crossref","first-page":"2140","DOI":"10.3390\/foods12112140","article-title":"Metagenomics: an effective approach for exploring microbial diversity and functions","volume":"12","author":"Nam","year":"2023","journal-title":"Foods"},{"key":"10.1016\/j.crmeth.2025.101266_bib2","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.rser.2018.10.021","article-title":"Bioinformatics analysis of metagenomics data of biogas-producing microbial communities in anaerobic digesters: A review","volume":"100","author":"Zhang","year":"2019","journal-title":"Renew. Sustain. Energy Rev."},{"key":"10.1016\/j.crmeth.2025.101266_bib3","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.scitotenv.2017.05.188","article-title":"Microbial community shifts in a farm-scale anaerobic digester treating swine waste: correlations between bacteria communities associated with hydrogenotrophic methanogens and environmental conditions","volume":"601\u2013602","author":"Cho","year":"2017","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.crmeth.2025.101266_bib4","doi-asserted-by":"crossref","first-page":"2868","DOI":"10.3389\/fimmu.2018.02868","article-title":"Exploring the human microbiome: the potential future role of next-generation sequencing in disease diagnosis and treatment","volume":"9","author":"Malla","year":"2018","journal-title":"Front. Immunol."},{"key":"10.1016\/j.crmeth.2025.101266_bib5","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1002\/lno.11382","article-title":"Linking metagenomics to aquatic microbial ecology and biogeochemical cycles","volume":"65","author":"Grossart","year":"2020","journal-title":"Limnol. Oceanogr."},{"key":"10.1016\/j.crmeth.2025.101266_bib6","doi-asserted-by":"crossref","DOI":"10.1016\/j.apsoil.2021.104047","article-title":"Soil metagenomics in grasslands and forests \u2013 A review and bibliometric analysis","volume":"167","author":"Vieira","year":"2021","journal-title":"Appl. Soil Ecol."},{"key":"10.1016\/j.crmeth.2025.101266_bib7","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-023-37016-0","article-title":"Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution","volume":"13","author":"Ohta","year":"2023","journal-title":"Sci. Rep."},{"key":"10.1016\/j.crmeth.2025.101266_bib8","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1038\/s41592-022-01539-7","article-title":"Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing","volume":"19","author":"Sereika","year":"2022","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2025.101266_bib9","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-022-08576-4","article-title":"Detecting structural variations with precise breakpoints using low-depth WGS data from a single Oxford Nanopore MinION flowcell","volume":"12","author":"Leung","year":"2022","journal-title":"Sci. Rep."},{"key":"10.1016\/j.crmeth.2025.101266_bib10","article-title":"Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome","volume":"9","author":"Shin","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.crmeth.2025.101266_bib11","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-10934-2","article-title":"Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps","volume":"10","author":"Dilthey","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.crmeth.2025.101266_bib12","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/s41592-022-01520-4","article-title":"Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data","volume":"19","author":"Curry","year":"2022","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2025.101266_bib13","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1101\/gr.210641.116","article-title":"Centrifuge: Rapid and sensitive classification of metagenomic sequences","volume":"26","author":"Kim","year":"2016","journal-title":"Genome Res."},{"key":"10.1016\/j.crmeth.2025.101266_bib14","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.crmeth.2025.101266_bib15","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s12859-024-05634-8","article-title":"Comparative analysis of metagenomic classifiers for long-read sequencing datasets","volume":"25","author":"Mari\u0107","year":"2024","journal-title":"BMC Bioinform"},{"key":"10.1016\/j.crmeth.2025.101266_bib16","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-024-49851-4","article-title":"Detection of hidden antibiotic resistance through real-time genomics","volume":"15","author":"Sauerborn","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.crmeth.2025.101266_bib17","doi-asserted-by":"crossref","first-page":"331","DOI":"10.3201\/eid2202.151796","article-title":"Nanopore sequencing as a rapidly deployable Ebola outbreak tool","volume":"22","author":"Hoenen","year":"2016","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.crmeth.2025.101266_bib18","doi-asserted-by":"crossref","first-page":"8525","DOI":"10.1038\/s41598-024-58768-3","article-title":"Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets","volume":"14","author":"Lim","year":"2024","journal-title":"Sci. Rep."},{"key":"10.1016\/j.crmeth.2025.101266_bib19","doi-asserted-by":"crossref","first-page":"e61504","DOI":"10.7554\/eLife.61504","article-title":"Freshwater monitoring by nanopore sequencing","volume":"10","author":"Urban","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.crmeth.2025.101266_bib20","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-18364-0","article-title":"Nanopore DNA sequencing and genome assembly on the International Space Station","volume":"7","author":"Castro-Wallace","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.crmeth.2025.101266_bib21","doi-asserted-by":"crossref","first-page":"2491","DOI":"10.3390\/w14162491","article-title":"Minion nanopore sequencing accelerates progress towards ubiquitous genetics in water research","volume":"14","author":"Werner","year":"2022","journal-title":"Water"},{"key":"10.1016\/j.crmeth.2025.101266_bib22","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1093\/bioinformatics\/btab780","article-title":"minoTour, real-time monitoring and analysis for nanopore sequencers","volume":"38","author":"Munro","year":"2022","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2025.101266_bib23","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btad492","article-title":"Nanoporeata: a user-friendly tool for nanopore-seq real-time transcriptional analysis","volume":"39","author":"Wierczeiko","year":"2023","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2025.101266_bib24","article-title":"Marti: a real-time analysis and visualisation tool for nanopore metagenomics","volume":"2025\u201302","author":"Peel","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.crmeth.2025.101266_bib25","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae108","article-title":"Nanometa live: a user-friendly application for real-time metagenomic data analysis and pathogen identification","volume":"40","author":"Sand\u00e5s","year":"2024","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2025.101266_bib26","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.65088","article-title":"Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with Biobakery 3","volume":"10","author":"Beghini","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.crmeth.2025.101266_bib27","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"Qiime allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2025.101266_bib28","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/978-1-4939-3369-3_13","article-title":"Mg-rast, a metagenomics service for analysis of microbial community structure and function","volume":"1399","author":"Keegan","year":"2016","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.crmeth.2025.101266_bib29","doi-asserted-by":"crossref","first-page":"W132","DOI":"10.1093\/nar\/gkac298","article-title":"BusyBee Web: towards comprehensive and differential composition-based metagenomic binning","volume":"50","author":"Schmartz","year":"2022","journal-title":"Nuc. Acids Res."},{"key":"10.1016\/j.crmeth.2025.101266_bib30","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-021-04089-5","article-title":"BugSeq: a highly accurate cloud platform for long-read metagenomic analyses","volume":"22","author":"Fan","year":"2021","journal-title":"BMC Bioinform"},{"key":"10.1016\/j.crmeth.2025.101266_bib31","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1186\/s12859-020-03684-2","article-title":"Maira\u2014real-time taxonomic and functional analysis of long reads on a laptop","volume":"21","author":"Albrecht","year":"2020","journal-title":"BMC Bioinform"},{"key":"10.1016\/j.crmeth.2025.101266_bib32","unstructured":"Oxford Nanopore Technologies. EPI2ME Labs. https:\/\/github.com\/epi2me-labs . Accessed: October 19, 2025."},{"key":"10.1016\/j.crmeth.2025.101266_bib33","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-021-04161-0","article-title":"BoardION: real-time monitoring of Oxford Nanopore sequencing instruments","volume":"22","author":"Bruno","year":"2021","journal-title":"BMC Bioinform"},{"key":"10.1016\/j.crmeth.2025.101266_bib34","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1186\/s12864-018-5094-y","article-title":"Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices","volume":"19","author":"Sanderson","year":"2018","journal-title":"BMC Genom."},{"key":"10.1016\/j.crmeth.2025.101266_bib35","series-title":"Human gut microbes under power-development of a bioelectrochemical system to uncouple and interrogate H2-syntrophic partners in the human gut microbiota","author":"Biehain","year":"2024"},{"key":"10.1016\/j.crmeth.2025.101266_bib36","doi-asserted-by":"crossref","DOI":"10.1126\/science.1254766","article-title":"Small molecules from the human microbiota","volume":"349","author":"Donia","year":"2015","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2025.101266_bib37","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nbt.3893","article-title":"Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea","volume":"35","author":"Bowers","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.crmeth.2025.101266_bib38","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1038\/s41592-023-01940-w","article-title":"Checkm2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning","volume":"20","author":"Chklovski","year":"2023","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2025.101266_bib39","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-022-05103-0","article-title":"Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets","volume":"23","author":"Portik","year":"2022","journal-title":"BMC Bioinform"},{"key":"10.1016\/j.crmeth.2025.101266_bib40","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s13062-018-0208-7","article-title":"MEGAN-LR: New algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs","volume":"13","author":"Huson","year":"2018","journal-title":"Biol. Direct"},{"key":"10.1016\/j.crmeth.2025.101266_bib41","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.1319","article-title":"Anvi\u2019o: an advanced analysis and visualization platform for \u2018omics data","volume":"3","author":"Eren","year":"2015","journal-title":"PeerJ"},{"key":"10.1016\/j.crmeth.2025.101266_bib42","doi-asserted-by":"crossref","first-page":"1411","DOI":"10.1093\/bioinformatics\/btx617","article-title":"Nephele: A cloud platform for simplified, standardized and reproducible microbiome data analysis","volume":"34","author":"Weber","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2025.101266_bib43","doi-asserted-by":"crossref","first-page":"4286","DOI":"10.1128\/IAI.00207-11","article-title":"Patric: The comprehensive bacterial bioinformatics resource with a focus on human pathogenic species","volume":"79","author":"Gillespie","year":"2011","journal-title":"Infect. Immun."},{"key":"10.1016\/j.crmeth.2025.101266_bib44","doi-asserted-by":"crossref","first-page":"D753","DOI":"10.1093\/nar\/gkac1080","article-title":"MGnify: the microbiome sequence data analysis resource in 2023","volume":"51","author":"Richardson","year":"2023","journal-title":"Nuc. Acids Res."},{"key":"10.1016\/j.crmeth.2025.101266_bib45","doi-asserted-by":"crossref","first-page":"1942","DOI":"10.3390\/genes13111942","article-title":"Unravelling metagenomics approach for microbial biofuel production","volume":"13","author":"Sartaj","year":"2022","journal-title":"Genes"},{"key":"10.1016\/j.crmeth.2025.101266_bib46","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.mib.2021.09.015","article-title":"Microbiomes for sustainable biomanufacturing","volume":"65","author":"Scarborough","year":"2022","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.crmeth.2025.101266_bib47","doi-asserted-by":"crossref","DOI":"10.1186\/s40168-019-0663-0","article-title":"Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing","volume":"7","author":"Che","year":"2019","journal-title":"Microbiome"},{"key":"10.1016\/j.crmeth.2025.101266_bib48","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00651-22","article-title":"A metagenomic investigation of spatial and temporal changes in sewage microbiomes across a university campus","volume":"7","author":"Fierer","year":"2022","journal-title":"mSystems"},{"key":"10.1016\/j.crmeth.2025.101266_bib49","doi-asserted-by":"crossref","first-page":"596","DOI":"10.3390\/min8120596","article-title":"Assessment of bioleaching microbial community structure and function based on next-generation sequencing technologies","volume":"8","author":"Zhou","year":"2018","journal-title":"Minerals"},{"key":"10.1016\/j.crmeth.2025.101266_bib50","doi-asserted-by":"crossref","DOI":"10.1128\/cmr.00103-22","article-title":"Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond","volume":"37","author":"Parkins","year":"2024","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.crmeth.2025.101266_bib51","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/s41564-022-01089-w","article-title":"Metagenomics-enabled microbial surveillance","volume":"7","author":"Ko","year":"2022","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.crmeth.2025.101266_bib52","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2025.101266_bib61","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1038\/s41592-020-00971-x","article-title":"metaFlye: scalable long-read metagenome assembly using repeat graphs","volume":"17","author":"Kolmogorov","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2025.101266_bib70","doi-asserted-by":"crossref","first-page":"e7359","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies","volume":"7","author":"Kang","year":"2019","journal-title":"PeerJ"},{"key":"10.1016\/j.crmeth.2025.101266_bib53","doi-asserted-by":"crossref","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: A toolkit to classify genomes with the genome taxonomy database","volume":"36","author":"Chaumeil","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2025.101266_bib54","article-title":"Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification","volume":"7","author":"Schwengers","year":"2021","journal-title":"Microb. Genom."},{"key":"10.1016\/j.crmeth.2025.101266_bib64","doi-asserted-by":"crossref","first-page":"1798","DOI":"10.1016\/j.csbj.2022.03.042","article-title":"UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets","volume":"20","author":"Sequeira","year":"2022","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.crmeth.2025.101266_bib55","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: Freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2025.101266_bib56","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-024-03244-4","article-title":"Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification","volume":"25","author":"Song","year":"2024","journal-title":"Genome Biol."},{"key":"10.1016\/j.crmeth.2025.101266_bib57","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1145\/382780.382782","article-title":"An analysis of the Burrows\u2014Wheeler transform","volume":"48","author":"Manzini","year":"2001","journal-title":"J. ACM"},{"key":"10.1016\/j.crmeth.2025.101266_bib58","series-title":"String Processing and Information Retrieval (SPIRE 2004), LNCS 3246","first-page":"150","article-title":"An alphabet-friendly fm-index","author":"Ferragina","year":"2004"},{"key":"10.1016\/j.crmeth.2025.101266_bib59","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1109\/79.543975","article-title":"The expectation-maximization algorithm","volume":"13","author":"Moon","year":"1996","journal-title":"IEEE Signal Process. Mag."},{"key":"10.1016\/j.crmeth.2025.101266_bib60","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/s40168-019-0665-y","article-title":"Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data","volume":"7","author":"Arumugam","year":"2019","journal-title":"Microbiome"},{"key":"10.1016\/j.crmeth.2025.101266_bib63","doi-asserted-by":"crossref","first-page":"D587","DOI":"10.1093\/nar\/gkac963","article-title":"KEGG for taxonomy-based analysis of pathways and genomes","volume":"51","author":"Kanehisa","year":"2023","journal-title":"Nuc. Acids Res."},{"key":"10.1016\/j.crmeth.2025.101266_bib65","author":"Django Software","year":"2024","journal-title":"Django"},{"key":"10.1016\/j.crmeth.2025.101266_bib66","doi-asserted-by":"crossref","unstructured":"Hossain, S. Visualization of Bioinformatics Data with Dash Bio (2019).","DOI":"10.25080\/Majora-7ddc1dd1-01f"},{"key":"10.1016\/j.crmeth.2025.101266_bib67","year":"2020","journal-title":"Pandas"},{"key":"10.1016\/j.crmeth.2025.101266_bib68","doi-asserted-by":"crossref","unstructured":"Mckinney, W. Data Structures for Statistical Computing in Python (2010).","DOI":"10.25080\/Majora-92bf1922-00a"},{"key":"10.1016\/j.crmeth.2025.101266_bib69","doi-asserted-by":"crossref","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","article-title":"Database resources of the National Center for Biotechnology Information","volume":"50","author":"Sayers","year":"2022","journal-title":"Nuc. Acids Res."}],"container-title":["Cell Reports Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237525003029?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237525003029?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T11:20:40Z","timestamp":1778930440000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2667237525003029"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":69,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["S2667237525003029"],"URL":"https:\/\/doi.org\/10.1016\/j.crmeth.2025.101266","relation":{},"ISSN":["2667-2375"],"issn-type":[{"value":"2667-2375","type":"print"}],"subject":[],"published":{"date-parts":[[2026,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"MMonitor for real-time monitoring of microbial communities using long reads","name":"articletitle","label":"Article Title"},{"value":"Cell Reports Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.crmeth.2025.101266","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"101266"}}