ArticleGenome biology2024
Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes.
Article in Genome biology, 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.
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- Genestrip: exact and efficient read classification for selected groups of organisms.BMC bioinformatics · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Dynamics of archaeal diversity and functionality in the piglet gut microbiome under common antimicrobial treatments.Frontiers in cellular and infection microbiology · 2026Article
- Combined NGS and proteomics improves viral diagnostics in wildlife: coronaviruses confirmed in hedgehogs.Frontiers in cellular and infection microbiology · 2026Article
- Limited consensus of marine viral diversity observed across techniques.Environmental microbiome · 2025Article
- Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.Briefings in bioinformatics · 2025Review
- Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.Microorganisms · 2025Review
- The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut.PLoS computational biology · 2025Article
- VirNucPro: an identifier for the identification of viral short sequences using six-frame translation and large language models.Briefings in bioinformatics · 2025Article
- Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples.Virology journal · 2025Article
- Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils.Microbiome · 2025Article
- BEREN: a bioinformatic tool for recovering giant viruses, polinton-like viruses, and virophages in metagenomic data.Bioinformatics advances · 2025Article
- ProkBERT PhaStyle: accurate phage lifestyle prediction with pretrained genomic language models.Bioinformatics advances · 2025Article
- AI-powered analysis of viral metagenomic sequencing data for rapid outbreak investigation and novel pathogen discovery.Frontiers in microbiology · 2025Review
- Viral metagenomic analysis of fecal samples fromFrontiers in cellular and infection microbiology · 2025Article
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Authors and funding
6 authors.
Funding
Abstract
backgroundAs most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance.
resultsWe compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered.
conclusionsTogether, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.
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