Marker-Delimited Codes for Short-Blocklength, High-Rate Coding over Multi-Read Edit Channels
Abstract
The read process of DNA-based data storage systems generates multiple noisy copies of the stored DNA sequences, affected by edit errors consisting of substitutions, deletions, and insertions. Motivated by the challenge of ensuring reliable data retrieval in the presence of edit errors, we present a concatenated coding scheme that accounts for practical design constraints in DNA storage. We introduce and apply the marker-delimited code (MDC) as the inner code, which enables fast and reliable computation of symbolwise a posteriori probabilities (APPs). We combine MDC with an outer LDPC code. The LDPC is decoded via belief propagation using the soft information generated by MDC. Our results show that, in comparison with prior work, this construction provides more efficient error correction over multi-read edit channels in the short-blocklength and high-rate regime.
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BibTeX
@misc{yercan2026markerdelimited,
title = {{Marker-Delimited Codes for Short-Blocklength, High-Rate Coding over Multi-Read Edit Channels}},
author = {Sinan Ates Yercan and Marc Antonini and Serge Kas Hanna},
howpublished = {arXiv},
year = {2026},
month = aug,
doi = {10.48550/arxiv.2608.30453},
eprint = {2608.30453},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2608.30453},
}
RIS
TY - UNPB
TI - Marker-Delimited Codes for Short-Blocklength, High-Rate Coding over Multi-Read Edit Channels
AU - Sinan Ates Yercan
AU - Marc Antonini
AU - Serge Kas Hanna
PY - 2026
DA - 2026/08/31
PB - arXiv
DO - 10.48550/arxiv.2608.30453
UR - https://arxiv.org/abs/2608.30453
AB - The read process of DNA-based data storage systems generates multiple noisy copies of the stored DNA sequences, affected by edit errors consisting of substitutions, deletions, and insertions. Motivated by the challenge of ensuring reliable data retrieval in the presence of edit errors, we present a concatenated coding scheme that accounts for practical design constraints in DNA storage. We introduce and apply the marker-delimited code (MDC) as the inner code, which enables fast and reliable computation of symbolwise a posteriori probabilities (APPs). We combine MDC with an outer LDPC code. The LDPC is decoded via belief propagation using the soft information generated by MDC. Our results show that, in comparison with prior work, this construction provides more efficient error correction over multi-read edit channels in the short-blocklength and high-rate regime.
ER -