ArticleGenome biology2022
viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 26 citations in OpenAlex.
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.NPJ biofilms and microbiomes · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- Review
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- Evaluation of a Probe-Based Enrichment Protocol for Nanopore Sequencing of Zoonotic Viruses.Viruses · 2025Article
- Article
- Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome.Nature communications · 2025Article
- Complete genome sequence ofMicrobiology resource announcements · 2025Article
- Review
- Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence.Neural regeneration research · 2024Review
- Article
- Hecatomb: an integrated software platform for viral metagenomics.GigaScience · 2024Article
- Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2023Review
- Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India.Virus research · 2023Article
- Complete Genome Sequence of Stutzerimonas stutzeri Strain SOCE 002, a Marine Bacterium Isolated from the Surface Seawater of Dapeng Bay.Microbiology resource announcements · 2023Article
- AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data.Bioinformatics (Oxford, England) · 2023Article
- Accuracy and Completeness of Long Read Metagenomic Assemblies.Microorganisms · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although the use of long-read sequencing improves the contiguity of assembled viral genomes compared to short-read methods, assembling complex viral communities remains an open problem. We describe the viralFlye tool for identification and analysis of metagenome-assembled viruses in long-read assemblies. We show it significantly improves viral assemblies and demonstrate that long-reads result in a much larger array of predicted virus-host associations as compared to short-read assemblies. We demonstrate that the identification of novel CRISPR arrays in bacterial genomes from a newly assembled metagenomic sample provides information for predicting novel hosts for novel viruses.
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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.