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arXiv · 2409.01223

Exact Error Exponents of Concatenated Codes for DNA Storage

Yan Hao Ling·Jonathan Scarlett
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Abstract

In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a ``black-box'' manner, and is only assumed to operate at an achievable rate in the sense of attaining asymptotically vanishing maximal (inner) error probability. We first derive the exact error exponent in a widely-studied regime of constant rate and a linear number of sequencing reads, and show strict improvements over an existing achievable error exponent. Moreover, our achievability analysis is based on a coded-index strategy, implying that such strategies attain the highest error exponents within the broader class of codes that we consider. We then extend our results to other scaling regimes, including a super-linear number of reads, as well as several certain low-rate regimes. We find that the latter comes with notable intricacies, such as the suboptimality of codewords with all distinct molecules, and certain dependencies of the error exponents on the model for sequencing errors.

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Yan Hao Ling, Jonathan Scarlett. 2025-06-18. Exact Error Exponents of Concatenated Codes for DNA Storage. https://arxiv.org/abs/2409.01223

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