Index-Based Concatenated Codes for the Multi-Draw DNA Storage Channel

TL;DR

This paper introduces an index-based concatenated coding scheme designed for DNA storage channels with complex error patterns, demonstrating improved error correction through a novel decoding approach and simulations.

Contribution

It proposes a new concatenated coding scheme with a joint index-synchronization decoder tailored for multi-draw DNA storage channels with IDS errors.

Findings

Achieves higher information rates for DNA storage channels.

Demonstrates effective error correction via Monte-Carlo simulations.

Provides a practical decoding method with optional clustering.

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 posterior probabilities for the outer decoder. We compute achievable information rates for the outer code and present Monte-Carlo simulations for information-outage probabilities and frame error rates on synthetic and experimental data, respectively.