ArticleMicrobiome2019
Choice of assembly software has a critical impact on virome characterisation.
Article in Microbiome, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
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Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Landscape of Genetic Content in the Gut and Oral Human Microbiome.Cell host & microbe · 2019Pooled it
- Evolving strategies for virus discovery.Microbial genomics · 2026Review
- Comparative genomic analysis of poly-γ-glutamic acid producing Bacillus licheniformis strains isolated from dairy products.Journal, genetic engineering & biotechnology · 2026Article
- Review
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Bacteriophages in gut metagenomes: from analysis to application.Virology journal · 2026Review
- A comparison of methods for the optimal recovery of the human fecal virome.ISME communications · 2026Article
- Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations.NAR genomics and bioinformatics · 2025Article
- Biases and complementarity in gut viromes obtained from bulk and virus-like particle-enriched metagenomic sequencing.Microbiology spectrum · 2025Article
- The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.European respiratory review : an official journal of the European Respiratory Society · 2025Review
- ViOTUcluster: A high-speed, All-in-one pipeline for viromic analysis of metagenomic data.iMetaOmics · 2025Article
- Lactococcal phage-host profiling through binding studies between cell wall polysaccharide types andMicrobial genomics · 2025Article
- Evaluation of Enrichment Approaches for the Study of the Viromes in Mollusk Species.Food and environmental virology · 2025Article
- Hard to jump: host shifts appear unlikely in a T4-like phage evolved in the lab.Frontiers in cellular and infection microbiology · 2025Article
- Bioinformatic Identification of Viral Genomes from High-Throughput Metagenomic Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners.Microbiome · 2024Article
- Article
- Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs.Microbiome · 2024Article
- Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics.Food and environmental virology · 2024Article
- Identification of distinct genotypes in circulating RSV A strains based on variants in the virus replication-associated genes.Journal of virology · 2024Article
30 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets.
designThis study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in human virome studies. Assemblers were assessed using four independent virome datasets, namely, simulated reads, two mock communities, viromes spiked with a known phage and human gut viromes.
resultsAssembly performance varied significantly across all test datasets, with SPAdes (meta) performing consistently well. Performance of MIRA and VICUNA varied, highlighting the importance of using a range of datasets when comparing assembly programs. It was also found that while some assemblers addressed the challenges of virome data better than others, all assemblers had limitations. Low read coverage and genomic repeats resulted in assemblies with poor genome recovery, high degrees of fragmentation and low-accuracy contigs across all assemblers. These limitations must be considered when setting thresholds for downstream analysis and when drawing conclusions from virome data.
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