ArticlePLoS computational biology2023
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing.
Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.
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113 citing papers in PubMed.
- A high-quality telomere-to-telomere lumpy skin disease virus genome assembly.The Journal of general virology · 2026Article
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- Adaptive Response ofAntibiotics (Basel, Switzerland) · 2026Article
- Anaerobic riboflavin degradation by human gutJournal of bacteriology · 2026Article
- Draft genomes ofMicrobiology resource announcements · 2026Article
- Revised complete genome sequences ofMicrobiology spectrum · 2026Article
- Performance of mechanically sheared DNA in multiplexed Oxford Nanopore sequencing forMicrobial genomics · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Chromosome-level genome assembly of Trichiurus japonicus resolves species boundaries and evolutionary history of cutlassfishes in Northwest Pacific.BMC genomics · 2026Article
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- A WGS workflow for identifying genetically modified and foodborne-pathogenicFood chemistry. Molecular sciences · 2026Article
- Barbell reveals and resolves demultiplexing and trimming issues in Nanopore data.Bioinformatics (Oxford, England) · 2026Article
- Complete genome ofMicrobiology resource announcements · 2026Article
- Exploring genetic variations and plasmid diversity in Escherichia coli strains isolated from Hospital Wastewater.BMC genomics · 2026Article
- Piperacillin-tazobactam resistance inAntimicrobial agents and chemotherapy · 2026Article
- Emerging zoonotic risks: whole-genome sequencing reveals antimicrobial resistance and genomic diversity in Providencia stuartii isolated from broiler chickens in Noakhali, Bangladesh.Poultry science · 2026Article
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Uncovering the ecophysiological potential of Motilimonas through genomic profiling analysis.BMC genomics · 2026Article
- Article
- Gene conversion is a key driver of diversity hotspots inbioRxiv : the preprint server for biology · 2026Article
53 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A perfect bacterial genome assembly is one where the assembled sequence is an exact match for the organism's genome-each replicon sequence is complete and contains no errors. While this has been difficult to achieve in the past, improvements in long-read sequencing, assemblers, and polishers have brought perfect assemblies within reach. Here, we describe our recommended approach for assembling a bacterial genome to perfection using a combination of Oxford Nanopore Technologies long reads and Illumina short reads: Trycycler long-read assembly, Medaka long-read polishing, Polypolish short-read polishing, followed by other short-read polishing tools and manual curation. We also discuss potential pitfalls one might encounter when assembling challenging genomes, and we provide an online tutorial with sample data (github.com/rrwick/perfect-bacterial-genome-tutorial).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.