ArticlemSystems2024
Benchmarking informatics approaches for virus discovery: caution is needed when combining
Article in mSystems, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 24 citations in OpenAlex.
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- Evolving strategies for virus discovery.Microbial genomics · 2026Review
- Convergent evolution of ST2 and ST164 mediates dissemination of the blaAnnals of clinical microbiology and antimicrobials · 2026Article
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- Insights from healthy mares reveal that mammalian uteri harbor a diverse virome.Scientific reports · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts.PLoS biology · 2026Article
- Diversity and ecological roles of hidden viral players in groundwater microbiomes.Nature communications · 2026Article
- Viromics approaches for the study of viral diversity and ecology in microbiomes.Nature reviews. Genetics · 2026Review
- Ecosystem health shapes viral ecology in peatland soils.Nature microbiology · 2026Article
- vir2vec: A Viral Genome-Wide Viral Embedding.bioRxiv : the preprint server for biology · 2025Article
- Genomic analysis of Androctonus mauritanicus toursvirus: first evidence of Ascoviridae in arachnids.Virus genes · 2025Article
- Genetic exchange networks bridge mobile DNA vehicles in the bacterial pathogen Listeria monocytogenes.Nature communications · 2025Article
- Gut Virome: What's the Role in Irritable Bowel Syndrome?Reviews in medical virology · 2025Review
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- Tracking putativemSystems · 2025Article
- Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.Briefings in bioinformatics · 2025Review
Corrections and comments
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Authors and funding
9 authors at 5 institutions in 2 countries.
Funding
Abstract
Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral identification tools. However, the effectiveness of this strategy is unknown. Here, we benchmarked combinations of six widely used informatics tools for viral identification and analysis (VirSorter, VirSorter2, VIBRANT, DeepVirFinder, CheckV, and Kaiju), called "rulesets." Rulesets were tested against mock metagenomes composed of taxonomically diverse sequence types and diverse aquatic metagenomes to assess the effects of the degree of viral enrichment and habitat on tool performance. We found that six rulesets achieved equivalent accuracy [Matthews Correlation Coefficient (MCC) = 0.77, IMPORTANCE: The identification of viruses from environmental metagenomes using informatics tools has offered critical insights in microbial ecology. However, it remains difficult for researchers to know which tools optimize viral recovery for their specific study. In an attempt to recover more viruses, studies are increasingly combining the outputs from multiple tools without validating this approach. After benchmarking combinations of six viral identification tools against mock metagenomes and environmental samples, we found that these tools should only be combined cautiously. Two to four tool combinations maximized viral recovery and minimized non-viral contamination compared with either the single-tool or the five- to six-tool ones. By providing a rigorous overview of the behavior of
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.