ArticleScientific reports2020
Benchmarking the MinION: Evaluating long reads for microbial profiling.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- A hybrid and cost-efficient barcoding strategy for full-length 16S rRNA gene nanopore sequencing of environmental samples.BMC genomics · 2026Article
- Rapid reconstruction of multidrug-resistant bacterial genomes using CycloneSEQ nanopore sequencing.iMetaOmics · 2026Article
- Real-time analysis and visualization of nanopore metagenomic samples with MARTi.Genome research · 2025Article
- SKiM: accurately classifying metagenomic ONT reads in limited memory.Bioinformatics (Oxford, England) · 2025Article
- A Practical Comparison of Short- and Long-Read Metabarcoding Sequencing: Challenges and Solutions for Plastid Read Removal and Microbial Community Exploration of Seaweed Samples.Molecular ecology resources · 2025Article
- PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking.GigaScience · 2025Article
- Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.Scientific data · 2024Article
- MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes.BMC bioinformatics · 2024Article
- The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.Microbial genomics · 2024Article
- Comparative analysis of metagenomic classifiers for long-read sequencing datasets.BMC bioinformatics · 2024Article
- Evaluation of Long-Read Sequencing Simulators to Assess Real-World Applications for Food Safety.Foods (Basel, Switzerland) · 2023Article
- Coriolis: enabling metagenomic classification on lightweight mobile devices.Bioinformatics (Oxford, England) · 2023Article
- Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing.Frontiers in microbiology · 2023Article
- Field-based detection of bacteria using nanopore sequencing: Method evaluation for biothreat detection in complex samples.PloS one · 2023Article
- Article
- Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets.BMC bioinformatics · 2022Article
- Metagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens.Ecology and evolution · 2022Article
- Article
- Metagenomic sequencing for detection and identification of the boxwood blight pathogen Calonectria pseudonaviculata.Scientific reports · 2022Article
- Evaluation of high molecular weight DNA extraction methods for long-read sequencing of Shiga toxin-producing Escherichia coli.PloS one · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nanopore based DNA-sequencing delivers long reads, thereby simplifying the decipherment of bacterial communities. Since its commercial appearance, this technology has been assigned several attributes, such as its error proneness, comparatively low cost, ease-of-use, and, most notably, aforementioned long reads. The technology as a whole is under continued development. As such, benchmarks are required to conceive, test and improve analysis protocols, including those related to the understanding of the composition of microbial communities. Here we present a dataset composed of twelve different prokaryotic species split into four samples differing by nucleic acid quantification technique to assess the specificity and sensitivity of the MinION nanopore sequencer in a blind study design. Taxonomic classification was performed by standard taxonomic sequence classification tools, namely Kraken, Kraken2 and Centrifuge directly on reads. This allowed taxonomic assignments of up to 99.27% on genus level and 92.78% on species level, enabling true-positive classification of strains down to 25,000 genomes per sample. Full genomic coverage is achieved for strains abundant as low as 250,000 genomes per sample under our experimental settings. In summary, we present an evaluation of nanopore sequence processing analysis with respect to microbial community composition. It provides an open protocol and the data may serve as basis for the development and benchmarking of future data processing pipelines.
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