R&D: Index-Based Concatenated Codes for Multi-Draw DNA Storage Channel

arxiv.org has published an article written by Lorenz Welter, School of Computation, Information and Technology, Technical University of Munich, DE-80333 Munich, Germany, Issam Maarouf, Simula UiB, N-5006 Bergen, Norway, Andreas Lenz, Antonia Wachter-Zeh, School of Computation, Information and Technology, Technical University of Munich, DE-80333 Munich, Germany, 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: “We consider error-correcting coding for DNA-based storage. We model the DNA storage channel as a multi-draw IDS channel where the input data is chunked into M short DNA strands, which are copied a random number of times, and the channel outputs a random selection of N noisy DNA strands. The retrieved DNA strands are prone to insertion, deletion, and substitution (IDS) errors. We propose an index-based concatenated coding scheme consisting of the concatenation of an outer code, an index code, and an inner synchronization code, where the latter two tackle IDS errors. We further propose a mismatched joint index-synchronization code maximum a posteriori probability decoder with optional clustering to infer symbolwise a posteriori probabilities for the outer decoder. We compute achievable information rates for the outer code and present Monte-Carlo simulations on experimental data.“