ArticleFrontiers in microbiology2014
Assembly of viral genomes from metagenomes.
Article in Frontiers in microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
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
33 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies.Briefings in bioinformatics · 2024Pooled it
- Detection of Wencheng shrew virus and cardiovirus from small mammals in Myanmar.Scientific reports · 2026Article
- Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics.Frontiers in microbiology · 2026Article
- AnViruses · 2025Article
- Genomic insights reveal community structure and phylogenetic associations of endohyphal bacteria and viruses in fungal endophytes.Environmental microbiome · 2025Article
- vClean: assessing virus sequence contamination in viral genomes.NAR genomics and bioinformatics · 2025Article
- Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.Viruses · 2025Article
- Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.PeerJ · 2025Article
- Article
- SegVir: Reconstruction of Complete Segmented RNA Viral Genomes from Metatranscriptomes.Molecular biology and evolution · 2024Article
- Viral genome sequencing methods: benefits and pitfalls of current approaches.Biochemical Society transactions · 2024Review
- ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data.Nature communications · 2023Article
- Genome binning of viral entities from bulk metagenomics data.Nature communications · 2022Article
- CheckV assesses the quality and completeness of metagenome-assembled viral genomes.Nature biotechnology · 2021Article
- Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities.Briefings in bioinformatics · 2021Article
- Enteric Virome and Carcinogenesis in the Gut.Digestive diseases and sciences · 2020Review
- Microbial and Viral Communities and Their Antibiotic Resistance Genes Throughout a Hospital Wastewater Treatment System.Frontiers in microbiology · 2020Article
- Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection.BMC infectious diseases · 2019Article
- Coding-Complete Genome Sequence of a Pollen-Associated Virus Belonging to theMicrobiology resource announcements · 2019Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity are, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.
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.