ArticleMicrobial genomics2021
Recovery of small plasmid sequences via Oxford Nanopore sequencing.
Article in Microbial genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Protocol for telomere-to-telomere assembly of Borrelia genomes using a hybrid method.STAR protocols · 2026Article
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- Filtering of artificial chimeric reads generated by ligation preparation method of nanopore sequencing.iScience · 2026Article
- Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia.The Journal of molecular diagnostics : JMD · 2026Article
- Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate.Microbial genomics · 2026Article
- Conference report: The Third Bacterial Genome Sequencing Pan-European Network conference.FEMS microbiology letters · 2026Article
- Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations.Antimicrobial agents and chemotherapy · 2025Review
- Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species.Briefings in bioinformatics · 2025Article
- Article
- Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing.Genome research · 2025Article
- Rapid whole genome sequencing for AMR surveillance in low- and middle-income countries: Oxford Nanopore Technology reveals multidrug-resistant Enterobacter cloacae complex from dairy farms in Sri Lanka.BMC veterinary research · 2025Article
- Influence of Sequencing Technology on Pangenome-Level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens.Open forum infectious diseases · 2025Article
- Deletion of pcnB affects antibiotic susceptibility in resistant Escherichia coli by reducing copy number of ColE1-family plasmids.Scientific reports · 2025Article
- High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy.Microbial genomics · 2025Article
- Host-pathogen protein interaction studies: quality control of cDNA libraries using nanopore sequencing.PloS one · 2025Article
- A genomics learning framework for undergraduates.PloS one · 2025Article
- Are reads required? High-precision variant calling from bacterial genome assemblies.Access microbiology · 2025Article
- Matching excellence: Oxford Nanopore Technologies' rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content.Microbial genomics · 2024Article
- Detection of hidden antibiotic resistance through real-time genomics.Nature communications · 2024Article
- Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies.Microbial genomics · 2024Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Oxford Nanopore Technologies (ONT) sequencing platforms currently offer two approaches to whole-genome native-DNA library preparation: ligation and rapid. In this study, we compared these two approaches for bacterial whole-genome sequencing, with a specific aim of assessing their ability to recover small plasmid sequences. To do so, we sequenced DNA from seven plasmid-rich bacterial isolates in three different ways: ONT ligation, ONT rapid and Illumina. Using the Illumina read depths to approximate true plasmid abundance, we found that small plasmids (<20 kbp) were underrepresented in ONT ligation read sets (by a mean factor of ~4) but were not underrepresented in ONT rapid read sets. This effect correlated with plasmid size, with the smallest plasmids being the most underrepresented in ONT ligation read sets. We also found lower rates of chimaeric reads in the rapid read sets relative to ligation read sets. These results show that when small plasmid recovery is important, ONT rapid library preparations are preferable to ligation-based protocols.
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