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Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length

Seong-Joon Park1, Sunghwan Kim2, Jaeho Jeong1

  • 1Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea.

Bioinformatics (Oxford, England)
|September 5, 2023
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Summary
This summary is machine-generated.

This study introduces novel encoding and decoding methods for DNA data storage, significantly reducing reading costs. The new approach enhances DNA storage efficiency and practicality for archival purposes.

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Area of Science:

  • Biotechnology
  • Data Storage
  • Bioinformatics

Background:

  • DNA-based data storage offers high density for archival needs but suffers from high writing and reading costs.
  • Existing DNA storage schemes require further cost reduction and optimization for practical application.

Purpose of the Study:

  • To develop cost-effective encoding and decoding procedures for DNA data storage.
  • To improve the efficiency and accuracy of DNA-based data retrieval.

Main Methods:

  • Implemented a novel encoding scheme using a single low-density parity-check (LDPC) code for error and dropout correction.
  • Developed advanced clustering and alignment methods for variable-length reads to enhance decoding.
  • Utilized edit distance and quality scores in sequence analysis-aided decoding to discard abnormal reads and leverage soft information.

Main Results:

  • Successfully stored 548.83 KB of an image file in DNA oligos.
  • Achieved a 7.46% reduction in writing costs.
  • Demonstrated significant reading cost reductions of 26.57% and 19.41% compared to previous methods.

Conclusions:

  • The proposed whole-process encoding and decoding procedures offer a more cost-effective solution for DNA data storage.
  • The developed methods improve the practicality of DNA storage for archival applications by reducing operational expenses.