ArticleMicrobial genomics2023
Long read genome assemblers struggle with small plasmids.
Article in Microbial genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Plasmidomics: studying plasmids as ecological entities beyond their hosts.Microbial genomics · 2026Review
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- Plasmid diversity, antibiotic resistance and virulence genes associated with Staphylococcus aureus isolates from private hospitals in Gauteng, South Africa.World journal of microbiology & biotechnology · 2026Article
- Exploratory Insights on Epidemiology, Genomic Features and Pangenome Analysis of NDM-1-Positive Carbapenem-ResistantAntibiotics (Basel, Switzerland) · 2026Article
- Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens.Microbial genomics · 2026Article
- Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate.Microbial genomics · 2026Article
- The Type III Secretion System plasmid pPHDPT3 of Photobacterium damselae subsp. piscicida is stable in Australian isolates due to conserved non-repetitive genomic architecture.FEMS microbiology letters · 2026Article
- Long-read sequencing reveals that the mitochondrial genome of an individualCurrent research in parasitology & vector-borne diseases · 2026Article
- Genomic safety, bacteriocinogenic potential, and probiotic-associated traits ofFrontiers in microbiology · 2026Article
- "Expanding the Lactococcal Cell Wall Polysaccharide Paradigm: Novel Structures and Metabolic Pathways in the Emerging Dairy Species Pseudolactococcus laudensis and Pseudolactococcus raffinolactis".MicrobiologyOpen · 2025Article
- ACCIO: An Assembly-Based Tool Enabling Plasmid Detection.medRxiv : the preprint server for health sciences · 2025Article
- Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species.Briefings in bioinformatics · 2025Article
- Lactococcal mobile genetic elements harbour a diverse phage defensome rich in restriction-modification systems.Nucleic acids research · 2025Article
- Autocycler: long-read consensus assembly for bacterial genomes.Bioinformatics (Oxford, England) · 2025Article
- Article
- An open-source nanopore-only sequencing workflow for analysis of clonal outbreaks delivers short-read level accuracy.Journal of clinical microbiology · 2025Article
- Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing.Genome research · 2025Article
- Inter- and intra-bacterial strain diversity remains the "elephant in the (living) room".npj antimicrobials and resistance · 2025Review
- Complete genomes of 568 diverseMicrobiology resource announcements · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
Whole-genome sequencing has become a preferred method for studying bacterial plasmids, as it is generally assumed to capture the entire genome. However, long-read genome assemblers have been shown to sometimes miss plasmid sequences - an issue that has been associated with plasmid size. The purpose of this study was to investigate the relationship between plasmid size and plasmid recovery by the long-read-only assemblers, Flye, Raven, Miniasm, and Canu. This was accomplished by determining the number of times each assembler successfully recovered 33 plasmids, ranging from 1919 to 194 062 bp in size and belonging to 14 bacterial isolates from six bacterial genera, using Oxford Nanopore long reads. These results were additionally compared to plasmid recovery rates by the short-read-first assembler, Unicycler, using both Oxford Nanopore long reads and Illumina short reads. Results from this study indicate that Canu, Flye, Miniasm, and Raven are prone to missing plasmid sequences, whereas Unicycler was successful at recovering 100 % of plasmid sequences. Excluding Canu, most plasmid loss by long-read-only assemblers was due to failure to recover plasmids smaller than 10 kb. As such, it is recommended that Unicycler be used to increase the likelihood of plasmid recovery during bacterial genome assembly.
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