ArticlePeerJ2021
Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation.
Article in PeerJ, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
66 citing papers in PubMed, 128 citations in OpenAlex.
- Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.Journal of advanced research · 2026Article
- Viruses help shape microbiome response to polyphenol rewiring of methane-suppressed peat microcosms.PLoS biology · 2026Article
- A diverse gut virome in natural populations of Drosophila melanogaster.Animal microbiome · 2026Article
- Review
- The Unified Human Virome Database: A toolkit for expanded human virome analysis.bioRxiv : the preprint server for biology · 2026Article
- V- and VNature communications · 2026Article
- Diversity, transfer potential, and transcriptional activity of virus-carried antibiotic resistance genes in global estuaries.iMetaOmics · 2026Article
- Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.Environmental science and ecotechnology · 2026Article
- Diversity and ecological roles of hidden viral players in groundwater microbiomes.Nature communications · 2026Article
- Bacteriophages in gut metagenomes: from analysis to application.Virology journal · 2026Review
- Ecosystem health shapes viral ecology in peatland soils.Nature microbiology · 2026Article
- Virus-encoded metabolism may support environmental stress adaptation of microbial hosts in an estuarine hypoxic zone.Frontiers in microbiology · 2026Article
- Viromics approaches for the study of viral diversity and ecology in microbiomes.Nature reviews. Genetics · 2026Review
- Viral diversity of brine and precipitated halite of Tuz Lake, an inland hypersaline lake in Turkey.Archives of virology · 2025Article
- Implementation and comparison of two concentration methods to detect and characterize bacteriophages and bacterial hosts from large drinking water samples.Environmental microbiome · 2025Article
- Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.Nature communications · 2025Article
- DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.bioRxiv : the preprint server for biology · 2025Article
- The association of the rumen virome with methane emissions in dairy cattle.Communications biology · 2025Article
- A call for caution in the biological interpretation of viral auxiliary metabolic genes.Nature microbiology · 2025Review
- Temporal dynamics, microdiversity, and ecological functions of viral communities during cyanobacterial blooms in Lake Taihu.NPJ biofilms and microbiomes · 2025Article
6 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
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundViruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs).
resultsThe in silico benchmarking of five commonly used virus identification tools show that gene-content-based tools consistently performed well for long (≥3 kbp) contigs, while
conclusionTogether, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses 'hidden' in diverse sequence datasets.
Indexed as
Identifiers
What OpenQuestion holds
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.