ArticleScientific data2019
Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.
Article in Scientific data, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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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.
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Who cites it
76 citing papers in PubMed.
- Microbial diversity and its links to retinol pathways and aroma compounds in ethnic fermented rice beverages of Assam.AMB Express · 2026Article
- Effects of short-term application of organic manure on the growth of forage maize (Zea mays L. cv. Kwangpyeongok) and soil bacterial communities.Scientific reports · 2026Article
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- PUDU (pipeline for universal diversity unveiling): an accessible end-to-end workflow for taxonomic profiling and ecological visualization of environmental microbiomes across amplicon, shotgun, and long-read sequencing.Frontiers in bioinformatics · 2026Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Limited consensus of marine viral diversity observed across techniques.Environmental microbiome · 2025Article
- Functional and genomic characterization of polyethylene degrading yeast Meyerozyma carpophila M6.0.2 isolated from marine plastic debris in East Java Indonesia.Scientific reports · 2025Article
- Adaptive sampling with Oxford Nanopore offers a simple way to improve the efficiency of plant metagenomic studies.The New phytologist · 2025Article
- How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study.Applied and environmental microbiology · 2025Article
- Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.Environment & health (Washington, D.C.) · 2025Review
- SKiM: accurately classifying metagenomic ONT reads in limited memory.Bioinformatics (Oxford, England) · 2025Article
- Comparison of Three DNA Isolation Methods and Two Sequencing Techniques for the Study of the Human Microbiota.Life (Basel, Switzerland) · 2025Article
- Jellyfish blooms-an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments.mSystems · 2025Article
- AI-powered analysis of viral metagenomic sequencing data for rapid outbreak investigation and novel pathogen discovery.Frontiers in microbiology · 2025Review
- Snow alga Sanguina aurantia as revealed through de novo genome assembly and annotation.G3 (Bethesda, Md.) · 2024Article
- Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.PLoS computational biology · 2024Article
- Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.Genome medicine · 2024Article
- Unveiling errors in soil microbial community sequencing: a case for reference soils and improved diagnostics for nanopore sequencing.Communications biology · 2024Article
- CAIM: coverage-based analysis for identification of microbiome.Briefings in bioinformatics · 2024Article
- Differential Reshaping of Skin and Intestinal Microbiota by Stocking Density and Oxygen Availability in Farmed Gilthead Sea Bream (Microorganisms · 2024Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors.
Funding
Abstract
Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.
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