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

文献类型： 外文期刊

第一作者： Ding, Lulu

作者： Ding, Lulu;Wu, Shigang;Hou, Zhihao;Li, Alun;Xu, Yaping;Feng, Hu;Pan, Weihua;Ruan, Jue;Hou, Zhihao

作者机构：

关键词： DNA digital storage (DDS); error-correcting code (ECC); soft-decision decoding; error-correcting capability; storage volume

期刊名称：NATIONAL SCIENCE REVIEW （ 影响因子：20.6； 五年影响因子：22.3 ）

ISSN： 2095-5138

年卷期： 2023 年

页码：

收录情况： SCI

摘要： Error-correcting codes (ECCs) employed in the state-of-the-art DNA digital storage (DDS) systems suffer from a trade-off between error-correcting capability and the proportion of redundancy. To address this issue, in this study, we introduce soft-decision decoding approach into DDS by proposing a DNA-specific error prediction model and a series of novel strategies. We demonstrate the effectiveness of our approach through a proof-of-concept DDS system based on Reed-Solomon (RS) code, named as Derrick. Derrick shows significant improvement in error-correcting capability without involving additional redundancy in both in vitro and in silico experiments, using various sequencing technologies such as Illumina, PacBio and Oxford Nanopore Technology (ONT). Notably, in vitro experiments using ONT sequencing at a depth of 7x reveal that Derrick, compared with the traditional hard-decision decoding strategy, doubles the error-correcting capability of RS code, decreases the proportion of matrices with decoding-failure by 229-fold, and amplifies the potential maximum storage volume by impressive 32 388-fold. Also, Derrick surpasses 'state-of-the-art' DDS systems by comprehensively considering the information density and the minimum sequencing depth required for complete information recovery. Crucially, the soft-decision decoding strategy and key steps of Derrick are generalizable to other ECCs' decoding algorithms. Though existing inspiring encoding strategies, the information density of DNA digital storage is limited by hard-decision decoding. By exploiting error bias in sequencing and alignment, soft-decision decoding with novel strategies doubles the error-correcting capability of RS code.

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