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Improving error-correcting capability in DNA digital storage via soft-decision decoding.

Lulu Ding1, Shigang Wu1, Zhihao Hou1,2

  • 1Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518120, China.

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Summary
This summary is machine-generated.

This study introduces a novel soft-decision decoding approach for DNA digital storage (DDS), enhancing error correction without adding redundancy. The Derrick system significantly boosts storage capacity and reliability across various sequencing technologies.

Keywords:
DNA digital storage (DDS)error-correcting capabilityerror-correcting code (ECC)soft-decision decodingstorage volume

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Area of Science:

  • Biotechnology
  • Information Science
  • Computer Science

Background:

  • Current DNA digital storage (DDS) systems face limitations with error-correcting codes (ECCs), balancing error correction against data redundancy.
  • A key challenge in DDS is improving error resilience without increasing storage overhead.

Purpose of the Study:

  • To introduce a soft-decision decoding approach for DDS to overcome the trade-off between error-correction capability and redundancy.
  • To develop a DNA-specific error prediction model and novel strategies for enhanced DDS performance.

Main Methods:

  • Proposed a soft-decision decoding approach integrated into a Reed-Solomon (RS) coded DDS system named Derrick.
  • Developed a DNA-specific error prediction model and novel decoding strategies.
  • Validated the approach using both in vitro and in silico experiments with Illumina, PacBio, and Oxford Nanopore Technology (ONT) sequencing.

Main Results:

  • The Derrick system demonstrated significantly improved error-correcting capability without additional redundancy.
  • In vitro experiments with ONT sequencing showed Derrick doubled RS code's error-correcting capability and reduced decoding failures by 229-fold.
  • The system amplified potential maximum storage volume by 32,388-fold and surpassed state-of-the-art DDS systems in information density and sequencing depth efficiency.

Conclusions:

  • The proposed soft-decision decoding strategy offers a substantial advancement for DNA digital storage.
  • Derrick's approach enhances storage capacity and reliability, outperforming existing DDS methods.
  • The soft-decision decoding strategy and Derrick's core components are generalizable to other ECC decoding algorithms.