ArticleMicrobial genomics2024
Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies.
Article in Microbial genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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87 citing papers in PubMed.
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- A subclade-associated genomic deletion encompassing vraDEH confers increased susceptibility to nisin A and bacitracin in Staphylococcus aureus CC121.Scientific reports · 2026Article
- Riboswitch-targeted improvement of lysine production in Bacillus and Priestia species.NPJ science of food · 2026Article
- Development of a stable low-copy mini F plasmid derivative for evaluating β-lactamase substrate specificity through antimicrobial susceptibility testing.Microbiology spectrum · 2026Article
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- Article
- Genomic and molecular characterisation of a KPC-producing Klebsiella pneumoniae clinical isolate resistant to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam.BMC genomic data · 2026Article
- Genome sequence ofMicrobiology resource announcements · 2026Article
- Performance of EUCAST disc diffusion and supplementary methods to detect reduced susceptibility to linezolid in enterococci- the NordicAST LRE-study.The Journal of antimicrobial chemotherapy · 2026Article
- Aliikangiella litoralis sp. nov. and Aliikangiella aequoris sp. nov., isolated from coastal seawaters of the Yellow Sea.Journal of microbiology (Seoul, Korea) · 2026Article
- Genome Mining Guided Identification of the Metallophore Delftichelin A fromJournal of natural products · 2026Article
- Cattle feces are a reservoir of diverse Acinetobacter species with potential to spread antibiotic resistance genes.Animal microbiome · 2026Article
27 more citing papers are in PubMed but not listed here.
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10 authors.
Funding
Abstract
Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants. They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.
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