ReviewFrontiers in microbiology2018
Overview of Virus Metagenomic Classification Methods and Their Biological Applications.
Review in Frontiers in microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
68 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Towards an understanding of the avian virome.The Journal of general virology · 2020Pooled it
- Virus Metagenomics in Farm Animals: A Systematic Review.Viruses · 2020Pooled it
- Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.International journal of environmental research and public health · 2025Article
- Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples.Virology journal · 2025Article
- Detection and genetic characterization of Uukuvirus lihanense (Uukuvirus, Phenuiviridae) in hard ticks from the Colombian Caribbean.Access microbiology · 2025Article
- Highly divergent and diverse viral community infecting sylvatic mosquitoes from Northeast Brazil.Journal of virology · 2024Article
- Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle.Veterinary research communications · 2024Review
- Longitudinal analysis of the enteric virome in paediatric subjects from the Free State Province, South Africa, reveals early gut colonisation and temporal dynamics.Virus research · 2024Article
- The effects of sequencing strategies on Metagenomic pathogen detection using bronchoalveolar lavage fluid samples.Heliyon · 2024Article
- Deepvirusclassifier: a deep learning tool for classifying SARS-CoV-2 based on viral subtypes within the coronaviridae family.BMC bioinformatics · 2024Article
- Metabuli: sensitive and specific metagenomic classification via joint analysis of amino acid and DNA.Nature methods · 2024Article
- Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data.Genome biology and evolution · 2024Article
- INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance.Genome medicine · 2024Article
- Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes.Genome biology · 2024Article
- Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake.Viruses · 2023Article
- Viral Diversity and Epidemiology in Critically Endangered Yangtze Finless Porpoises (Neophocaena asiaeorientalisMicrobiology spectrum · 2023Article
- Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments.Journal of microbiology (Seoul, Korea) · 2023Review
- Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses.Viruses · 2023Review
- Novel Virus Identification through Metagenomics: A Systematic Review.Life (Basel, Switzerland) · 2022Review
- Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.Microorganisms · 2022Review
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomics poses opportunities for clinical and public health virology applications by offering a way to assess complete taxonomic composition of a clinical sample in an unbiased way. However, the techniques required are complicated and analysis standards have yet to develop. This, together with the wealth of different tools and workflows that have been proposed, poses a barrier for new users. We evaluated 49 published computational classification workflows for virus metagenomics in a literature review. To this end, we described the methods of existing workflows by breaking them up into five general steps and assessed their ease-of-use and validation experiments. Performance scores of previous benchmarks were summarized and correlations between methods and performance were investigated. We indicate the potential suitability of the different workflows for (1) time-constrained diagnostics, (2) surveillance and outbreak source tracing, (3) detection of remote homologies (discovery), and (4) biodiversity studies. We provide two decision trees for virologists to help select a workflow for medical or biodiversity studies, as well as directions for future developments in clinical viral metagenomics.
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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.