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Integrated optimization of experimental and computational workflows improves genome recovery in long-read gut metagenomics

  • Y. Hu
  • L. Sun
  • Y. Huang
  • F. Jiang
  • X. Tong
  • J. Yang
  • Y. Ju
  • Z. Yang
  • S. Liufu
  • Y. Hu
  • W. Ma
  • R. Guo
4 more authors
  • W. Li
  • T. Zhang
  • X. Zhu1
  • Z. Zhang
  1. 1School of Artificial Intelligence,Jianghan University,Wuhan,China.
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Abstract

Short-read metagenomic sequencing has been widely applied in microbial research due to its high quality and decreasing cost. However, short reads are inherently fragmented, which limits assembly contiguity and the recovery of complete microbial genomes. In contrast, long-read sequencing, with significantly longer read lengths, helps overcome these limitations. Achieving complete and accurate genome recovery is the core goal of metagenomics. To address this challenge, we systematically evaluated and optimized the long-read metagenomic workflow, from sample processing to computational assembly, using the CycloneSEQ platform.

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Cite

BibTeXRIS
BibTeX
@misc{hu2026integrated,
  title = {{Integrated optimization of experimental and computational workflows improves genome recovery in long-read gut metagenomics}},
  author = {Y. Hu and L. Sun and Y. Huang and F. Jiang and X. Tong and J. Yang and Y. Ju and Z. Yang and S. Liufu and Y. Hu and W. Ma and R. Guo and W. Li and T. Zhang and X. Zhu and Z. Zhang},
  howpublished = {bioRxiv},
  year = {2026},
  month = may,
  doi = {10.64898/2026.05.22.727065},
  url = {https://www.biorxiv.org/content/10.64898/2026.05.22.727065v2},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Integrated optimization of experimental and computational workflows improves genome recovery in long-read gut metagenomics
AU  - Y. Hu
AU  - L. Sun
AU  - Y. Huang
AU  - F. Jiang
AU  - X. Tong
AU  - J. Yang
AU  - Y. Ju
AU  - Z. Yang
AU  - S. Liufu
AU  - Y. Hu
AU  - W. Ma
AU  - R. Guo
AU  - W. Li
AU  - T. Zhang
AU  - X. Zhu
AU  - Z. Zhang
PY  - 2026
DA  - 2026/05/22
PB  - bioRxiv
DO  - 10.64898/2026.05.22.727065
UR  - https://www.biorxiv.org/content/10.64898/2026.05.22.727065v2
AB  - Short-read metagenomic sequencing has been widely applied in microbial research due to its high quality and decreasing cost. However, short reads are inherently fragmented, which limits assembly contiguity and the recovery of complete microbial genomes. In contrast, long-read sequencing, with significantly longer read lengths, helps overcome these limitations. Achieving complete and accurate genome recovery is the core goal of metagenomics. To address this challenge, we systematically evaluated and optimized the long-read metagenomic workflow, from sample processing to computational assembly, using the CycloneSEQ platform.
ER  -