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Composite Hedges Nanopores codec system for rapid and portable DNA data readout with high INDEL-Correction

Author

Listed:
  • Xuyang Zhao

    (Southern University of Science and Technology)

  • Junyao Li

    (Southern University of Science and Technology)

  • Qingyuan Fan

    (Southern University of Science and Technology)

  • Jing Dai

    (Southern University of Science and Technology)

  • Yanping Long

    (Southern University of Science and Technology)

  • Ronghui Liu

    (Southern University of Science and Technology)

  • Jixian Zhai

    (Southern University of Science and Technology)

  • Qing Pan

    (Zhejiang University of Technology)

  • Yi Li

    (Southern University of Science and Technology)

Abstract

Reading digital information from highly dense but lightweight DNA medium nowadays relies on time-consuming next-generation sequencing. Nanopore sequencing holds the promise to overcome the efficiency problem, but high indel error rates lead to the requirement of large amount of high quality data for accurate readout. Here we introduce Composite Hedges Nanopores, capable of handling indel rates up to 15.9% and substitution rates up to 7.8%. The overall information density can be doubled from 0.59 to 1.17 by utilizing a degenerated eight-letter alphabet. We demonstrate that sequencing times of 20 and 120 minutes are sufficient for processing representative text and image files, respectively. Moreover, to achieve complete data recovery, it is estimated that text and image data require 4× and 8× physical redundancy of composite strands, respectively. Our codec system excels on both molecular design and equalized dictionary usage, laying a solid foundation approaching to real-time DNA data retrieval and encoding.

Suggested Citation

  • Xuyang Zhao & Junyao Li & Qingyuan Fan & Jing Dai & Yanping Long & Ronghui Liu & Jixian Zhai & Qing Pan & Yi Li, 2024. "Composite Hedges Nanopores codec system for rapid and portable DNA data readout with high INDEL-Correction," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53455-3
    DOI: 10.1038/s41467-024-53455-3
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    Cited by:

    1. Zihui Yan & Guanjin Qu & Xin Chen & Gang Zheng & Huaming Wu, 2025. "DNA StairLoop: enabling high-fidelity data recovery and robust error correction in DNA-based data storage," Nature Communications, Nature, vol. 16(1), pages 1-10, December.
    2. Junyao Li & Xuyang Zhao & Qingyuan Fan & Yanping Long & Ronghui Liu & Jixian Zhai & Qing Pan & Yi Li, 2025. "Empowering low-crosstalk, dynamic-decision random access of DNA storage via 384-multiplexed nanopore signatures," Nature Communications, Nature, vol. 16(1), pages 1-12, December.

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