ArticleScientific reports2021
Comparative evaluation of Nanopore polishing tools for microbial genome assembly and polishing strategies for downstream analysis.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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58 citing papers in PubMed.
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- Comparative Genome Analysis of Illumina, Nanopore, and Hybrid Approaches: A Case Study of the Aquaculture Isolate 160P.Pathogens (Basel, Switzerland) · 2026Article
- Leishmania donovani's protein tyrosine phosphatases interact with DUF21 and respond to environmental magnesium.The FEBS journal · 2026Article
- From ecology to evolution: plasmid- and colicin-mediated persistence of antibiotic-resistantmSystems · 2026Article
- Genome-wide association study bridging genomics-phenomics gap in natural plant populations.Journal of applied genetics · 2026Review
- High-risk lineages shape the resistome and virulome of multidrug-resistantFrontiers in cellular and infection microbiology · 2026Article
- Quantitative phage-host interaction profiling supports the design of a broadly active phage cocktail against multidrug-resistantFrontiers in microbiology · 2026Article
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- Isolation and characterization ofFrontiers in microbiology · 2026Article
- Hybrid Genome Sequencing and Comparative Analysis of Three NovelFoods (Basel, Switzerland) · 2025Article
- Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation ofJournal of clinical microbiology · 2025Article
- Phylogenetic and functional diversity amongmSystems · 2025Article
- Protozoal populations drive system-wide variation in the rumen microbiome.Nature communications · 2025Article
- Constraints in temperature adaptation reinforce differences in thermal niche between mesophilic and psychrotolerantProceedings. Biological sciences · 2025Article
- Hybrid sequencing reveals the genome of a Chrysochromulina parva virus and highlight its distinct replication strategy.BMC genomics · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- GoldPolish-target: targeted long-read genome assembly polishing.BMC bioinformatics · 2025Article
- Evaluation of whole-genome sequencing protocols for detection of antimicrobial resistance, virulence factors and mobile genetic elements in antimicrobial-resistant bacteria.Journal of medical microbiology · 2025Article
- Complete genome sequence ofMicrobiology resource announcements · 2025Article
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Authors and funding
10 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Assembling high-quality microbial genomes using only cost-effective Nanopore long-read systems such as Flongle is important to accelerate research on the microbial genome and the most critical point for this is the polishing process. In this study, we performed an evaluation based on BUSCO and Prokka gene prediction in terms of microbial genome assembly for eight state-of-the-art Nanopore polishing tools and combinations available. In the evaluation of individual tools, Homopolish, PEPPER, and Medaka demonstrated better results than others. In combination polishing, the second round Homopolish, and the PEPPER × medaka combination also showed better results than others. However, individual tools and combinations have specific limitations on usage and results. Depending on the target organism and the purpose of the downstream research, it is confirmed that there remain some difficulties in perfectly replacing the hybrid polishing carried out by the addition of a short-read. Nevertheless, through continuous improvement of the protein pores, related base-calling algorithms, and polishing tools based on improved error models, a high-quality microbial genome can be achieved using only Nanopore reads without the production of additional short-read data. The polishing strategy proposed in this study is expected to provide useful information for assembling the microbial genome using only Nanopore reads depending on the target microorganism and the purpose of the research.
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