Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies

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.

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Publication Details

Journal
Gigabyte
Published
2025-04-25
DOI
https://doi.org/10.46471/gigabyte.154
Citations
10
Primary Topic
Genomics and Phylogenetic Studies
Type
article
Field-Weighted Citation Impact
8.06

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article

Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies

Liang Xiao, Ruijin Guo, Tongyuan Hu, Yanmei Ju et al.
10 citations
Gigabyte
Genomics and Phylogenetic Studies
8.06
article

Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies

Liang Xiao, Ruijin Guo, Tongyuan Hu, Yanmei Ju, Chuanyu Liu, Yuanqiang Zou, Fei Guo, Hewei Liang, Haoyu Wang, Xin Jin, Bo Wang, Xun Xu, Wenwei Zhang, Yuliang Dong, Zeng Tao, Junyi Chen, Yuning Zhang, Mengmeng Wang, Wenxin He
article en
10 citations

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.

GigabyteVol. 2025
Botswana Geoscience Institute (BW), University of Chinese Academy of Sciences (CN), BGI Research (CN)
Government of Jiangxi Province
Life in Land
Openalex Percentile: Top 2%
Genomics and Phylogenetic Studies
8.06
DOIOpen Access PDFOpenAlex
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