ArticleGigaByte (Hong Kong, China)2025
Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies.
Article in GigaByte (Hong Kong, China), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- Review
- Complete genome sequence of a newMicrobiology resource announcements · 2026Article
- Mechanisms of constipation alleviation by Lacticaseibacillus paracasei BGI-N2: insights from genes to phenotypes.BMC microbiology · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Review
- The applications and advantages of nanopore sequencing in bacterial antimicrobial resistance surveillance and research.npj antimicrobials and resistance · 2025Review
- De novo non-canonical nanopore basecalling enables private communication using heavily-modified DNA data at single-molecule level.Nature communications · 2025Article
- Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation.GigaScience · 2025Article
- Revealing the potent probiotic properties and alcohol degradation capabilities ofFrontiers in microbiology · 2025Article
- Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies.GigaByte (Hong Kong, China) · 2025Article
Corrections and comments
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current microbial sequencing relies on short-read platforms like Illumina and DNBSEQ, which are cost-effective and accurate but often produce fragmented draft genomes. Here, we used CycloneSEQ for long-read sequencing of ATCC BAA-835, producing long-reads with an average length of 11.6 kbp and an average quality score of 14.4. Hybrid assembly with short-reads data resulted in an error rate of only 0.04 mismatches and 0.08 indels per 100 kbp compared to the reference genome. This method, validated across nine species, successfully assembled complete circular genomes. Hybrid assembly significantly enhances genome completeness by using long-reads to fill gaps and accurately assembling multi-copy rRNA genes, unlike short-reads alone. Data subsampling showed that combining over 500 Mbp of short-read data with 100 Mbp of long-read data yields high-quality circular assemblies. CycloneSEQ long-reads improves the assembly of circular complete genomes from mixed microbial communities; however, its base quality needs improving. Integrating DNBSEQ short-reads improved accuracy, resulting in complete and accurate assemblies.
Identifiers
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Registered trials
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.