Concatenated Codes for Multiple Reads of a DNA Sequence

Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a concatenated coding scheme with an outer nonbinary low-dens...

Full description

Saved in:
Bibliographic Details
Published in:arXiv.org 2022-09
Main Authors: Maarouf, Issam, Lenz, Andreas, Welter, Lorenz, Wachter-Zeh, Antonia, Rosnes, Eirik, Alexandre Graell i Amat
Format: Article
Language:English
Subjects:
Algorithms
Codes
Concatenated codes
Critical components
Data storage
Decoding
Deoxyribonucleic acid
DNA
Error correcting codes
Gene sequencing
Markov chains
Performance evaluation
Storage systems
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a concatenated coding scheme with an outer nonbinary low-density parity-check code or a polar code and either an inner convolutional code or a time-varying block code. We propose two novel decoding algorithms for inference from multiple received sequences, both combining the inner code and channel to a joint hidden Markov model to infer symbolwise a posteriori probabilities (APPs). The first decoder computes the exact APPs by jointly decoding the received sequences, whereas the second decoder approximates the APPs by combining the results of separately decoded received sequences and has a complexity that is linear with the number of sequences. Using the proposed algorithms, we evaluate the performance of decoding multiple received sequences by means of achievable information rates and Monte-Carlo simulations. We show significant performance gains compared to a single received sequence. In addition, we succeed in improving the performance of the aforementioned coding scheme by optimizing both the inner and outer codes.
ISSN:2331-8422