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Robust data storage in DNA by de Bruijn graph-based de novo strand assembly

Author

Listed:
  • Lifu Song

    (Tianjin University
    Tianjin University)

  • Feng Geng

    (Binzhou Medical University)

  • Zi-Yi Gong

    (Tianjin University
    Tianjin University)

  • Xin Chen

    (Tianjin University)

  • Jijun Tang

    (Tianjin University
    Chinese Academy of Sciences)

  • Chunye Gong

    (National SuperComputer Center in Tianjin)

  • Libang Zhou

    (Nanjing Agricultural University)

  • Rui Xia

    (National SuperComputer Center in Tianjin)

  • Ming-Zhe Han

    (Tianjin University
    Tianjin University)

  • Jing-Yi Xu

    (Tianjin University
    Tianjin University)

  • Bing-Zhi Li

    (Tianjin University
    Tianjin University)

  • Ying-Jin Yuan

    (Tianjin University
    Tianjin University)

Abstract

DNA data storage is a rapidly developing technology with great potential due to its high density, long-term durability, and low maintenance cost. The major technical challenges include various errors, such as strand breaks, rearrangements, and indels that frequently arise during DNA synthesis, amplification, sequencing, and preservation. In this study, a de novo strand assembly algorithm (DBGPS) is developed using de Bruijn graph and greedy path search to meet these challenges. DBGPS shows substantial advantages in handling DNA breaks, rearrangements, and indels. The robustness of DBGPS is demonstrated by accelerated aging, multiple independent data retrievals, deep error-prone PCR, and large-scale simulations. Remarkably, 6.8 MB of data is accurately recovered from a severely corrupted sample that has been treated at 70 °C for 70 days. With DBGPS, we are able to achieve a logical density of 1.30 bits/cycle and a physical density of 295 PB/g.

Suggested Citation

  • Lifu Song & Feng Geng & Zi-Yi Gong & Xin Chen & Jijun Tang & Chunye Gong & Libang Zhou & Rui Xia & Ming-Zhe Han & Jing-Yi Xu & Bing-Zhi Li & Ying-Jin Yuan, 2022. "Robust data storage in DNA by de Bruijn graph-based de novo strand assembly," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33046-w
    DOI: 10.1038/s41467-022-33046-w
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    References listed on IDEAS

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