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

• 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.

Ämnesord

TEKNIK OCH TEKNOLOGIER  -- Elektroteknik och elektronik -- Telekommunikation (hsv//swe)

ENGINEERING AND TECHNOLOGY  -- Electrical Engineering, Electronic Engineering, Information Engineering -- Telecommunications (hsv//eng)

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