ArticlePeerJ2019
virMine: automated detection of viral sequences from complex metagenomic samples.
Article in PeerJ, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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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.
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Who cites it
28 citing papers in PubMed.
- VITALdb: to select the best viroinformatics tools for a desired virus or application.Briefings in bioinformatics · 2025Article
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Benchmarking informatics approaches for virus discovery: caution is needed when combiningmSystems · 2024Article
- Tips and tools to obtain and assess mosquito viromes.Archives of microbiology · 2024Review
- Metagenomic Identification of Novel Eukaryotic Viruses with Small DNA Genomes in Pheasants.Animals : an open access journal from MDPI · 2024Article
- Hecatomb: an integrated software platform for viral metagenomics.GigaScience · 2024Article
- Review
- Current trends in RNA virus detection through metatranscriptome sequencing data.FEBS open bio · 2023Review
- Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data.Microbiome · 2023Article
- Evaluation of computational phage detection tools for metagenomic datasets.Frontiers in microbiology · 2023Article
- Development and Validation of a Bioinformatic Workflow for the Rapid Detection of Viruses in Biosecurity.Viruses · 2022Article
- Revolutionized virome research using systems microbiology approaches.Experimental biology and medicine (Maywood, N.J.) · 2022Review
- virMine 2.0: Identifying Viral Sequences in Microbial Communities.Microbiology resource announcements · 2022Article
- Urinary Tract Virome as an Urgent Target for Metagenomics.Life (Basel, Switzerland) · 2021Review
- Utilizing the VirIdAl Pipeline to Search for Viruses in the Metagenomic Data of Bat Samples.Viruses · 2021Article
- DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach.GigaScience · 2021Article
- Simulation study and comparative evaluation of viral contiguous sequence identification tools.BMC bioinformatics · 2021Article
- Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins.Scientific reports · 2021Article
- Experimental approaches to tracking mobile genetic elements in microbial communities.FEMS microbiology reviews · 2020Review
- Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types.Virus evolution · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.
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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.