References

Baltimore, David. 1971. “Expression of Animal Virus Genomes.” Bacteriological Reviews 35 (3): 235–41. https://doi.org/10.1128/br.35.3.235-241.1971.
Bin Jang, Ho, Benjamin Bolduc, Olivier Zablocki, Jens H. Kuhn, Simon Roux, Evelien M. Adriaenssens, J. Rodney Brister, et al. 2019. “Taxonomic Assignment of Uncultivated Prokaryotic Virus Genomes Is Enabled by Gene-Sharing Networks.” Nature Biotechnology 37: 632–39. https://doi.org/10.1038/s41587-019-0100-8.
Bolger, Anthony M., Marc Lohse, and Bjoern Usadel. 2014. “Trimmomatic: A Flexible Trimmer for Illumina Sequence Data.” Bioinformatics 30 (15): 2114–20. https://doi.org/10.1093/bioinformatics/btu170.
Camargo, Antonio Pedro, Simon Roux, Frederik Schulz, Michal Babinski, Yan Xu, Bin Hu, Patrick S. G. Chain, Stephen Nayfach, and Nikos C. Kyrpides. 2024. “Identification of Mobile Genetic Elements with geNomad.” Nature Biotechnology 42: 1303–12. https://doi.org/10.1038/s41587-023-01953-y.
Cantalapiedra, Carlos P., Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, and Jaime Huerta-Cepas. 2021. “eggNOG-Mapper V2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale.” Molecular Biology and Evolution 38 (12): 5825–29. https://doi.org/10.1093/molbev/msab293.
Chen, Shifu, Yanqing Zhou, Yaru Chen, and Jia Gu. 2018. “Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor.” Bioinformatics 34 (17): i884–90. https://doi.org/10.1093/bioinformatics/bty560.
Danecek, Petr, James K. Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O. Pollard, Andrew Whitwham, et al. 2021. “Twelve Years of SAMtools and BCFtools.” GigaScience 10 (2): giab008. https://doi.org/10.1093/gigascience/giab008.
Fu, Limin, Beifang Niu, Zhengwei Zhu, Sitao Wu, and Weizhong Li. 2012. “CD-HIT: Accelerated for Clustering the Next-Generation Sequencing Data.” Bioinformatics 28 (23): 3150–52. https://doi.org/10.1093/bioinformatics/bts565.
Galiez, Clément, Matthias Siebert, François Enault, Jonathan Vincent, and Johannes Söding. 2017. “WIsH: Who Is the Host? Predicting Prokaryotic Hosts from Metagenomic Phage Contigs.” Bioinformatics 33 (19): 3113–14. https://doi.org/10.1093/bioinformatics/btx383.
Guo, Jiarong, Benjamin Bolduc, Ahmed A. Zayed, Arvind Varsani, Gabriela Dominguez-Huerta, Tom O. Delmont, Akbar A. Pratama, et al. 2021. “VirSorter2: A Multi-Classifier, Expert-Guided Approach to Detect Diverse DNA and RNA Viruses.” Microbiome 9: 37. https://doi.org/10.1186/s40168-020-00990-y.
Gurevich, Alexey, Vladislav Saveliev, Nikolay Vyahhi, and Glenn Tesler. 2013. “QUAST: Quality Assessment Tool for Genome Assemblies.” Bioinformatics 29 (8): 1072–75. https://doi.org/10.1093/bioinformatics/btt086.
Hyatt, Doug, Gwo-Liang Chen, Philip F. LoCascio, Miriam L. Land, Frank W. Larimer, and Loren J. Hauser. 2010. “Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification.” BMC Bioinformatics 11: 119. https://doi.org/10.1186/1471-2105-11-119.
International Committee on Taxonomy of Viruses. 2026. “ICTV Taxonomy.” https://ictv.global/taxonomy.
Katoh, Kazutaka, and Daron M. Standley. 2013. “MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability.” Molecular Biology and Evolution 30 (4): 772–80. https://doi.org/10.1093/molbev/mst010.
Kieft, Kristopher, Zhichao Zhou, and Karthik Anantharaman. 2020. “VIBRANT: Automated Recovery, Annotation and Curation of Microbial Viruses, and Evaluation of Viral Community Function from Genomic Sequences.” Microbiome 8: 90. https://doi.org/10.1186/s40168-020-00867-0.
Langmead, Ben, and Steven L. Salzberg. 2012. “Fast Gapped-Read Alignment with Bowtie 2.” Nature Methods 9 (4): 357–59. https://doi.org/10.1038/nmeth.1923.
Li, Dinghua, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, and Tak-Wah Lam. 2015. “MEGAHIT: An Ultra-Fast Single-Node Solution for Large and Complex Metagenomics Assembly via Succinct de Bruijn Graph.” Bioinformatics 31 (10): 1674–76. https://doi.org/10.1093/bioinformatics/btv033.
Minh, Bui Quang, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf, Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear. 2020. “IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.” Molecular Biology and Evolution 37 (5): 1530–34. https://doi.org/10.1093/molbev/msaa015.
Minot, Samuel, Rohini Sinha, Jun Chen, Hongzhe Li, Sue A. Keilbaugh, Gary D. Wu, James D. Lewis, and Frederic D. Bushman. 2011. “The Human Gut Virome: Inter-Individual Variation and Dynamic Response to Diet.” Genome Research 21 (10): 1616–25. https://doi.org/10.1101/gr.122705.111.
Nayfach, Stephen, Antonio Pedro Camargo, Frederik Schulz, Emiley Eloe-Fadrosh, Simon Roux, and Nikos C. Kyrpides. 2021. “CheckV Assesses the Quality and Completeness of Metagenome-Assembled Viral Genomes.” Nature Biotechnology 39: 578–85. https://doi.org/10.1038/s41587-020-00774-7.
NCBI. 2026. “Sequence Read Archive.” https://www.ncbi.nlm.nih.gov/sra.
NCBI Sequence Read Archive. 2022. “Download SRA Sequences from Entrez Search Results.” https://www.ncbi.nlm.nih.gov/sra/docs/sradownload.
———. 2024. “SRA Run SRR29680455, BioProject PRJNA527877, Experiment SRX25183710.” https://www.ncbi.nlm.nih.gov/sra.
Nurk, Sergey, Dmitry Meleshko, Anton Korobeynikov, and Pavel A. Pevzner. 2017. “metaSPAdes: A New Versatile Metagenomic Assembler.” Genome Research 27 (5): 824–34. https://doi.org/10.1101/gr.213959.116.
Posit. 2024. “Quarto Documentation.” https://quarto.org/docs/books/.
Ren, Jie, Nathan A. Ahlgren, Yang Young Lu, Jed A. Fuhrman, and Fengzhu Sun. 2017. “VirFinder: A Novel k-Mer Based Tool for Identifying Viral Sequences from Assembled Metagenomic Data.” Microbiome 5: 69. https://doi.org/10.1186/s40168-017-0283-5.
Ren, Jie, Kai Song, Chao Deng, Nathan A. Ahlgren, Jed A. Fuhrman, Yi Li, Xiaohui Xie, Ryan Poplin, and Fengzhu Sun. 2020. “Identifying Viruses from Metagenomic Data Using Deep Learning.” Quantitative Biology 8 (1): 64–77. https://doi.org/10.1007/s40484-019-0187-4.
Roux, Simon, Evelien M. Adriaenssens, Bas E. Dutilh, Eugene V. Koonin, Andrew M. Kropinski, Mart Krupovic, Jens H. Kuhn, et al. 2019. “Minimum Information about an Uncultivated Virus Genome (MIUViG).” Nature Biotechnology 37: 29–37. https://doi.org/10.1038/nbt.4306.
Roux, Simon, Antonio Pedro Camargo, Felipe H. Coutinho, Shareef M. Dabdoub, Bas E. Dutilh, et al. 2023. “iPHoP: An Integrated Machine Learning Framework to Maximize Host Prediction for Metagenome-Derived Viruses of Archaea and Bacteria.” PLOS Biology 21 (4): e3002083. https://doi.org/10.1371/journal.pbio.3002083.
Roux, Simon, Francois Enault, Bonnie L. Hurwitz, and Matthew B. Sullivan. 2015. “VirSorter: Mining Viral Signal from Microbial Genomic Data.” PeerJ 3: e985. https://doi.org/10.7717/peerj.985.
Shaffer, Michael, Mikayla A. Borton, Brendan B. McGivern, Ahmed A. Zayed, Sabina L. La Rosa, Lindsey M. Solden, Pengfei Liu, et al. 2020. “DRAM for Distilling Microbial Metabolism to Automate the Curation of Microbiome Function.” Nucleic Acids Research 48 (16): 8883–8900. https://doi.org/10.1093/nar/gkaa621.
Shang, Jiayu, Cheng Peng, Jiaojiao Guan, Dehan Cai, Donglin Wang, and Yanni Sun. 2026. “PhaBOX2: An Enhanced Web Server for Discovering and Analyzing Viral Contigs in Metagenomic Data.” Nucleic Acids Research 54: W169–76. https://doi.org/10.1093/nar/gkag382.
Shen, Wei, Shuai Le, Yan Li, and Fuquan Hu. 2016. “SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/q File Manipulation.” PLOS ONE 11 (10): e0163962. https://doi.org/10.1371/journal.pone.0163962.
Zielezinski, Andrzej, Adam Gudyś, Jakub Barylski, Krzysztof Siminski, Piotr Rozwalak, Bas E. Dutilh, and Sebastian Deorowicz. 2025. “Ultrafast and Accurate Sequence Alignment and Clustering of Viral Genomes.” Nature Methods 22: 1191–94. https://doi.org/10.1038/s41592-025-02701-7.