{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T23:52:23Z","timestamp":1770076343946,"version":"3.49.0"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T00:00:00Z","timestamp":1764892800000},"content-version":"vor","delay-in-days":34,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Swiss State Secretariat for Education, Research and Innovation","award":["22.00210"],"award-info":[{"award-number":["22.00210"]}]},{"name":"European Union nor European Research Executive Agency"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce \u201cViromeXplore,\u201d a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https:\/\/github.com\/rhernandvel\/ViromeXplore.<\/jats:p>","DOI":"10.1093\/bib\/bbaf638","type":"journal-article","created":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T13:07:30Z","timestamp":1762952850000},"source":"Crossref","is-referenced-by-count":1,"title":["ViromeXplore: integrative workflows for complete and reproducible virome characterization"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-3048-8573","authenticated-orcid":false,"given":"Rodrigo","family":"Hern\u00e1ndez-Vel\u00e1zquez","sequence":"first","affiliation":[{"name":"Department of Health Sciences and Technology, ETH Zurich , R\u00e4mistrasse 101, 8092 Zurich ,","place":["Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michal","family":"Ziemski","sequence":"additional","affiliation":[{"name":"Department of Health Sciences and Technology, ETH Zurich , R\u00e4mistrasse 101, 8092 Zurich ,","place":["Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1784-8935","authenticated-orcid":false,"given":"Nicholas A","family":"Bokulich","sequence":"additional","affiliation":[{"name":"Department of Health Sciences and Technology, ETH Zurich , R\u00e4mistrasse 101, 8092 Zurich ,","place":["Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,12,5]]},"reference":[{"key":"2026020206562750400_ref1","doi-asserted-by":"publisher","first-page":"1864","DOI":"10.1038\/s41467-024-45793-z","article-title":"A metagenomic catalog of the early-life human gut virome","volume":"15","author":"Zeng","year":"2024","journal-title":"Nat Commun"},{"key":"2026020206562750400_ref2","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1038\/s41564-023-01564-y","article-title":"The gut virome is associated with stress-induced changes in behaviour and immune responses in mice","volume":"9","author":"Ritz","year":"2024","journal-title":"Nat Microbiol"},{"key":"2026020206562750400_ref3","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1038\/nature19366","article-title":"Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses","volume":"537","author":"Roux","year":"2016","journal-title":"Nature"},{"key":"2026020206562750400_ref4","doi-asserted-by":"publisher","first-page":"e67667","DOI":"10.7554\/eLife.67667","article-title":"Unifying the known and unknown microbial coding sequence space","volume":"11","author":"Vanni","year":"2022","journal-title":"elife"},{"key":"2026020206562750400_ref5","doi-asserted-by":"publisher","first-page":"16532","DOI":"10.1038\/srep16532","article-title":"Modular approach to customise sample preparation procedures for viral metagenomics: A reproducible protocol for virome analysis","volume":"5","author":"Concei\u00e7\u00e3o-Neto","year":"2015","journal-title":"Sci Rep"},{"key":"2026020206562750400_ref6","doi-asserted-by":"publisher","first-page":"4126","DOI":"10.1093\/bioinformatics\/btaa490","article-title":"MetaviralSPAdes: Assembly of viruses from metagenomic data","volume":"36","author":"Antipov","year":"2020","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref7","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s40168-020-00990-y","article-title":"VirSorter2: A multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses","volume":"9","author":"Guo","year":"2021","journal-title":"Microbiome"},{"key":"2026020206562750400_ref8","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s40168-017-0283-5","article-title":"VirFinder: A novel k-mer based tool for identifying viral sequences from assembled metagenomic data","volume":"5","author":"Ren","year":"2017","journal-title":"Microbiome"},{"key":"2026020206562750400_ref9","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1038\/s41587-019-0100-8","article-title":"Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks","volume":"37","author":"Bin Jang","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026020206562750400_ref10","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giac110","article-title":"What the phage: A scalable workflow for the identification and analysis of phage sequences","volume":"11","author":"Marquet","year":"2022","journal-title":"Gigascience"},{"key":"2026020206562750400_ref11","doi-asserted-by":"publisher","first-page":"e1011422","DOI":"10.1371\/journal.pcbi.1011422","article-title":"VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models","volume":"19","author":"Rangel-Pineros","year":"2023","journal-title":"PLoS Comput Biol"},{"key":"2026020206562750400_ref12","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1099\/mgen.0.001202","article-title":"ViromeFlowX: A comprehensive Nextflow-based automated workflow for mining viral genomes from metagenomic sequencing data","volume":"10","author":"Wang","year":"2024","journal-title":"Microb Genom"},{"key":"2026020206562750400_ref13","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2026020206562750400_ref14","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00888-24","article-title":"MVP: A modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes","volume":"9","author":"Coclet","year":"2024","journal-title":"mSystems"},{"key":"2026020206562750400_ref15","doi-asserted-by":"publisher","first-page":"23774","DOI":"10.1038\/srep23774","article-title":"VIP: An integrated pipeline for metagenomics of virus identification and discovery","volume":"6","author":"Li","year":"2016","journal-title":"Sci Rep"},{"key":"2026020206562750400_ref16","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giae065","article-title":"V-pipe 3.0: A sustainable pipeline for within-sample viral genetic diversity estimation","volume":"13","author":"Fuhrmann","year":"2024","journal-title":"Gigascience"},{"key":"2026020206562750400_ref17","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa086","article-title":"A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level","volume":"9","author":"Pratas","year":"2020","journal-title":"Gigascience"},{"key":"2026020206562750400_ref18","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026020206562750400_ref19","doi-asserted-by":"publisher","first-page":"e1011676","DOI":"10.1371\/journal.pcbi.1011676","article-title":"Facilitating bioinformatics reproducibility with QIIME 2 provenance replay","volume":"19","author":"Keefe","year":"2023","journal-title":"PLoS Comput Biol"},{"key":"2026020206562750400_ref20","doi-asserted-by":"publisher","DOI":"10.1101\/2025.01.27.635007","volume-title":"MOSHPIT: Accessible, Reproducible Metagenome Data Science on the QIIME 2 Framework","author":"Ziemski","year":"2025"},{"key":"2026020206562750400_ref21","doi-asserted-by":"publisher","first-page":"1408","DOI":"10.1038\/s41587-019-0334-5","article-title":"Detecting contamination in viromes using ViromeQC","volume":"37","author":"Zolfo","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026020206562750400_ref22","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1038\/s41587-023-01953-y","article-title":"Identification of mobile genetic elements with geNomad","volume":"42","author":"Camargo","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2026020206562750400_ref23","doi-asserted-by":"publisher","first-page":"8","DOI":"10.3390\/v8030066","article-title":"Linking virus genomes with host taxonomy","volume":"8","author":"Mihara","year":"2016","journal-title":"Viruses"},{"key":"2026020206562750400_ref24","doi-asserted-by":"crossref","first-page":"11257","DOI":"10.1038\/ncomms11257","article-title":"Fast and sensitive taxonomic classification for metagenomics with Kaiju","volume":"7","author":"Menzel","year":"2016","journal-title":"Nat Commun"},{"key":"2026020206562750400_ref25","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1186\/1471-2105-12-385","article-title":"Interactive metagenomic visualization in a web browser","volume":"12","author":"Ondov","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2026020206562750400_ref26","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref27","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref28","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","article-title":"CheckV assesses the quality and completeness of metagenome-assembled viral genomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2026020206562750400_ref29","doi-asserted-by":"publisher","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref30","doi-asserted-by":"crossref","first-page":"6788","DOI":"10.1038\/s41467-024-51230-y","article-title":"Unveiling the unknown viral world in groundwater","volume":"15","author":"Wu","year":"2024","journal-title":"Nat Commun"},{"key":"2026020206562750400_ref31","doi-asserted-by":"crossref","first-page":"5254","DOI":"10.1038\/s41467-023-41075-2","article-title":"Interrogating the viral dark matter of the rumen ecosystem with a global virome database","volume":"14","author":"Yan","year":"2023","journal-title":"Nat Commun"},{"key":"2026020206562750400_ref32","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1016\/j.cell.2019.03.040","article-title":"Marine DNA viral macro- and microdiversity from pole to pole","volume":"177","author":"Gregory","year":"2019","journal-title":"Cell"},{"key":"2026020206562750400_ref33","doi-asserted-by":"publisher","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: A versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"2026020206562750400_ref34","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: Functional annotation, Orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2026020206562750400_ref35","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat Methods"},{"key":"2026020206562750400_ref36","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026020206562750400_ref37","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2026020206562750400_ref38","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"2026020206562750400_ref39","doi-asserted-by":"publisher","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":"2026020206562750400_ref40","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/s41564-023-01598-2","article-title":"COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes","volume":"9","author":"Chen","year":"2024","journal-title":"Nat Microbiol"},{"key":"2026020206562750400_ref41","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2020.102002","article-title":"Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean","volume":"24","author":"Kaneko","year":"2021","journal-title":"iScience"},{"key":"2026020206562750400_ref42","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1016\/j.cels.2019.08.002","article-title":"Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data","volume":"9","author":"Tackmann","year":"2019","journal-title":"Cell Syst"},{"key":"2026020206562750400_ref43","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive tree of life (iTOL) v6: Recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026020206562750400_ref44","doi-asserted-by":"publisher","DOI":"10.1128\/msphere.00585-18","article-title":"Gut Virome analysis of Cameroonians reveals high diversity of enteric viruses, including potential interspecies transmitted viruses","volume":"4","author":"Yinda","year":"2019","journal-title":"mSphere"},{"key":"2026020206562750400_ref45","doi-asserted-by":"publisher","first-page":"5081","DOI":"10.1093\/bioinformatics\/btac639","article-title":"Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue","volume":"38","author":"Ziemski","year":"2022","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref46","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: Architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2026020206562750400_ref47","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref48","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","article-title":"ART: A next-generation sequencing read simulator","volume":"28","author":"Huang","year":"2012","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref49","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1093\/bioinformatics\/btv697","article-title":"MetaQUAST: Evaluation of metagenome assemblies","volume":"32","author":"Mikheenko","year":"2016","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref50","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1016\/j.cell.2019.07.010","article-title":"Benchmarking metagenomics tools for taxonomic classification","volume":"178","author":"Ye","year":"2019","journal-title":"Cell"},{"key":"2026020206562750400_ref51","doi-asserted-by":"crossref","first-page":"bbad087","DOI":"10.1093\/bib\/bbad087","article-title":"Benchmarking genome assembly methods on metagenomic sequencing data","volume":"24","author":"Zhang","year":"2023","journal-title":"Brief Bioinform"},{"key":"2026020206562750400_ref52","first-page":"156","article-title":"Cryptic and abundant marine viruses at the evolutionary origins of Earth\u2019s RNA virome","volume":"2022","author":"Zayed","year":"1979","journal-title":"Science"},{"key":"2026020206562750400_ref53","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1186\/s12859-022-05052-8","article-title":"Persistent memory as an effective alternative to random access memory in metagenome assembly","volume":"23","author":"Sun","year":"2022","journal-title":"BMC Bioinformatics"},{"key":"2026020206562750400_ref54","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1186\/s40168-023-01533-x","article-title":"Gauge your phage: Benchmarking of bacteriophage identification tools in metagenomic sequencing data","volume":"11","author":"Ho","year":"2023","journal-title":"Microbiome"},{"key":"2026020206562750400_ref55","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2018.00304","article-title":"MARVEL, a tool for prediction of bacteriophage sequences in metagenomic bins","volume":"9","author":"Amgarten","year":"2018","journal-title":"Front Genet"},{"key":"2026020206562750400_ref56","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat Commun"},{"key":"2026020206562750400_ref57"},{"key":"2026020206562750400_ref58","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1016\/j.cell.2019.01.001","article-title":"Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle","volume":"176","author":"Pasolli","year":"2019","journal-title":"Cell"},{"key":"2026020206562750400_ref59","doi-asserted-by":"publisher","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast genome-wide functional annotation through Orthology assignment by eggNOG-mapper","volume":"34","author":"Huerta-Cepas","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2026020206562750400_ref60","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":"2026020206562750400_ref61","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref62","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1101\/gr.213959.116","article-title":"metaSPAdes: A new versatile metagenomic assembler","volume":"27","author":"Nurk","year":"2017","journal-title":"Genome Res"},{"key":"2026020206562750400_ref63","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giz066","article-title":"PPR-meta: A tool for identifying phages and plasmids from metagenomic fragments using deep learning","volume":"8","author":"Fang","year":"2019","journal-title":"Gigascience"},{"key":"2026020206562750400_ref64","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaf147","article-title":"CoverM: Read alignment statistics for metagenomics","volume":"41","author":"Aroney","year":"2025","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref65","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: A flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref66","doi-asserted-by":"crossref","first-page":"W200","DOI":"10.1093\/nar\/gky448","article-title":"HMMER web server: 2018 update","volume":"46","author":"Potter","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026020206562750400_ref67","doi-asserted-by":"publisher","first-page":"D1020","DOI":"10.1093\/nar\/gkaa1105","article-title":"RefSeq: Expanding the prokaryotic genome annotation pipeline reach with protein family model curation","volume":"49","author":"Li","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026020206562750400_ref68","doi-asserted-by":"publisher","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The Pfam protein families database: Towards a more sustainable future","volume":"44","author":"Finn","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026020206562750400_ref69"},{"key":"2026020206562750400_ref70","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1093\/bioinformatics\/btu739","article-title":"UniRef clusters: A comprehensive and scalable alternative for improving sequence similarity searches","volume":"31","author":"Suzek","year":"2015","journal-title":"Bioinformatics"},{"key":"2026020206562750400_ref71","doi-asserted-by":"publisher","first-page":"S427","DOI":"10.1093\/infdis\/jiac426","article-title":"The Picornaviridae family: Knowledge gaps, animal models, countermeasures, and prototype pathogens","volume":"228","author":"Andino","year":"2023","journal-title":"J Infect Dis"},{"key":"2026020206562750400_ref72","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00522-20","article-title":"Fermented-food metagenomics reveals substrate-associated differences in taxonomy and health-associated and antibiotic resistance determinants","volume":"5","author":"Leech","year":"2020","journal-title":"mSystems"},{"key":"2026020206562750400_ref73","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1016\/j.idairyj.2011.06.003","article-title":"A new phage on the \u2018mozzarella\u2019 block: Bacteriophage 5093 shares a low level of homology with other Streptococcus thermophilus phages","volume":"21","author":"Mills","year":"2011","journal-title":"Int Dairy J"},{"key":"2026020206562750400_ref74","doi-asserted-by":"publisher","first-page":"D708","DOI":"10.1093\/nar\/gkx932","article-title":"Virus taxonomy: The database of the International Committee on Taxonomy of Viruses (ICTV)","volume":"46","author":"Lefkowitz","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026020206562750400_ref75","doi-asserted-by":"publisher","first-page":"111342","DOI":"10.1016\/j.foodres.2022.111342","article-title":"Prevalence of bacterial genes in the phage fraction of food viromes","volume":"156","author":"Blanco-Picazo","year":"2022","journal-title":"Food Res Int"},{"key":"2026020206562750400_ref76","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1038\/s41586-020-1957-x","article-title":"Giant virus diversity and host interactions through global metagenomics","volume":"578","author":"Schulz","year":"2020","journal-title":"Nature"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/6\/bbaf638\/65779713\/bbaf638.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/6\/bbaf638\/65779713\/bbaf638.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T11:56:35Z","timestamp":1770033395000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaf638\/8371886"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,1]]},"references-count":76,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2025,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaf638","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,11]]},"published":{"date-parts":[[2025,11,1]]},"article-number":"bbaf638"}}