An Efficient Joint Decoding Scheme for Outer Codes in DNA-Based Data Storage

In this paper, we consider a simplified system model for DNA-based data storage, where each DNA string is either correctly transmitted, or being erased, or being corrupted by random substitution errors, and all strings are randomly shuffled with each other. Any linear block error-correction code can be used as the outer code to encode bits among different strings. We derive soft/hard information of all bits, which allows to independently decode each bit within a string, leading to an independent decoding scheme. To improve the decoding performance, we measure the reliability of each string based on the independent decoding result, and perform a further step of decoding over the most reliable strings, leading to a joint decoding scheme. Simulations with low-density parity-check codes confirm that the joint decoding scheme can reduce the frame error rate by more than 3 orders of magnitude compared to the independent decoding scheme.