ArticleViruses2023
Enhanced Viral Metagenomics with Lazypipe 2.
Article in Viruses, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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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.
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Who cites it
16 citing papers in PubMed, 24 citations in OpenAlex.
- Metagenomic Characterization and Molecular Screening of Pathogens in Freshwater Amphipods (Pathogens (Basel, Switzerland) · 2026Article
- A solinvivirus induces cellular antiviral responses and reduces the lifespan of adult black soldier flies.The Journal of general virology · 2026Article
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- Genetic characterization of rat hepatitis E virus (Rocahepevirus ratti) in urban brown rats (Rattus norvegicus) in Helsinki, Finland.Archives of virology · 2025Article
- Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification.mSystems · 2025Article
- Improving the reporting of metagenomic virome-scale data.Communications biology · 2024Article
- Detection of divergent Orthohantavirus tulaense provides insight into wide host range and viral evolutionary patterns.Npj viruses · 2024Article
- VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.Molecular biology and evolution · 2024Article
- Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance.Nature communications · 2024Article
- Complete coding sequence of an Aedes flavivirus strain isolated fromMicrobiology resource announcements · 2024Article
- ViralFlow v1.0-a computational workflow for streamlining viral genomic surveillance.NAR genomics and bioinformatics · 2024Article
- Epstein-Barr Virus in the Cerebrospinal Fluid and Blood Compartments of Patients With Multiple Sclerosis and Controls.Neurology(R) neuroimmunology & neuroinflammation · 2024Article
- Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security.Microorganisms · 2024Review
- Ten common issues with reference sequence databases and how to mitigate them.Frontiers in bioinformatics · 2024Review
- Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses are the main agents causing emerging and re-emerging infectious diseases. It is therefore important to screen for and detect them and uncover the evolutionary processes that support their ability to jump species boundaries and establish themselves in new hosts. Metagenomic next-generation sequencing (mNGS) is a high-throughput, impartial technology that has enabled virologists to detect either known or novel, divergent viruses from clinical, animal, wildlife and environmental samples, with little a priori assumptions. mNGS is heavily dependent on bioinformatic analysis, with an emerging demand for integrated bioinformatic workflows. Here, we present Lazypipe 2, an updated mNGS pipeline with, as compared to Lazypipe1, significant improvements in code stability and transparency, with added functionality and support for new software components. We also present extensive benchmarking results, including evaluation of a novel canine simulated metagenome, precision and recall of virus detection at varying sequencing depth, and a low to extremely low proportion of viral genetic material. Additionally, we report accuracy of virus detection with two strategies: homology searches using nucleotide or amino acid sequences. We show that Lazypipe 2 with nucleotide-based annotation approaches near perfect detection for eukaryotic viruses and, in terms of accuracy, outperforms the compared pipelines. We also discuss the importance of homology searches with amino acid sequences for the detection of highly divergent novel viruses.
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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.