ReviewFrontiers in microbiology2015
Recovering full-length viral genomes from metagenomes.
Review in Frontiers in microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics.Frontiers in microbiology · 2026Article
- Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.PeerJ · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data.Virus evolution · 2024Article
- Comparison of Source Attribution Methodologies for Human Campylobacteriosis.Pathogens (Basel, Switzerland) · 2023Article
- Enhanced Viral Metagenomics with Lazypipe 2.Viruses · 2023Article
- Taxonomic, functional and expression analysis of viral communities associated with marine sponges.PeerJ · 2021Article
- Setting a baseline for global urban virome surveillance in sewage.Scientific reports · 2020Article
- Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types.Virus evolution · 2020Article
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- Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes.Frontiers in microbiology · 2018Article
- Overview of Virus Metagenomic Classification Methods and Their Biological Applications.Frontiers in microbiology · 2018Review
- Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases.Frontiers in microbiology · 2017Article
- Viral metagenomics and blood safety.Transfusion clinique et biologique : journal de la Societe francaise de transfusion sanguine · 2016Review
- Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine.Frontiers in physiology · 2016Review
- HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts.Frontiers in microbiology · 2016Article
- GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data.Frontiers in microbiology · 2016Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Infectious disease metagenomics is driven by the question: "what is causing the disease?" in contrast to classical metagenome studies which are guided by "what is out there?" In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.
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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.