R&D: Achievable Information Rates and Concatenated Codes for DNA Nanopore Sequencing Channel

arxiv.org has published an article written by Issam Maarouf, Eirik Rosnes, Simula UiB, N-5006 Bergen, Norway, and Alexandre Graell i Amat, Department of Electrical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.

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.“