Achievable Information Rates and Concatenated Codes for the DNA Nanopore Sequencing Channel

Issam Maarouf; Eirik Rosnes; Alexandre Graell i Amat

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arXiv · 2212.07287

Achievable Information Rates and Concatenated Codes for the DNA Nanopore Sequencing Channel

Issam Maarouf·Eirik Rosnes·Alexandre Graell i Amat

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Abstract

The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et al., which models the inherent memory of the channel. We derive the maximum a posteriori (MAP) decoder for this channel model. The derived MAP decoder allows us to compute achievable information rates for the true DNA storage channel assuming a mismatched decoder matched to the memory-$k$ nanopore channel model, and quantify the loss in performance assuming a small memory length--and hence limited decoding complexity. Furthermore, the derived MAP decoder can be used to design error-correcting codes tailored to the DNA storage channel. We show that a concatenated coding scheme with an outer low-density parity-check code and an inner convolutional code yields excellent performance.

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Issam Maarouf, Eirik Rosnes, Alexandre Graell i Amat. 2022-12-14. Achievable Information Rates and Concatenated Codes for the DNA Nanopore Sequencing Channel. https://arxiv.org/abs/2212.07287

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