Optimized code design for constrained DNA data storage with asymmetric errors

Deng, Li; Wang, Yixin; Noor-A-Rahim, Md.; Guan, Yong Liang; Shi, Zhiping; Gunawan, Erry; Poh, Chueh Loo

Optimized code design for constrained DNA data storage with asymmetric errors

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Files

08746106.pdf(7.07 MB)

Published version

Date

2019-06-26

Authors

Deng, Li

Wang, Yixin

Noor-A-Rahim, Md.

Guan, Yong Liang

Shi, Zhiping

Gunawan, Erry

Poh, Chueh Loo

Publisher

Institute of Electrical and Electronics Engineers Inc.

Published Version

10.1109/ACCESS.2019.2924827

Abstract

With ultra-high density and preservation longevity, deoxyribonucleic acid (DNA)-based data storage is becoming an emerging storage technology. Limited by the current biochemical techniques, data might be corrupted during the processes of DNA data storage. A hybrid coding architecture consisting of modified variable-length run-length limited (VL-RLL) codes and optimized protograph low-density parity-check (LDPC) codes is proposed in order to suppress error occurrence and correct asymmetric substitution errors. Based on the analyses of the different asymmetric DNA sequencer channel models, a series of the protograph LDPC codes are optimized using a modified extrinsic information transfer algorithm (EXIT). The simulation results show the better error performance of the proposed protograph LDPC codes over the conventional good codes and the codes used in the existing DNA data storage system. In addition, the theoretical analysis shows that the proposed hybrid coding scheme stores ~1.98 bits per nucleotide (bits/nt) with only 1% gap from the upper boundary (2 bits/nt).

Keywords

Channel coding , DNA , Parity check codes , Runlength codes , DNA data storage system , Asymmetric DNA sequencer channel models , Hybrid coding scheme stores , Error performance , Modified extrinsic information transfer algorithm , Protograph LDPC codes , Correct asymmetric substitution errors , Error occurrence , Optimized protograph low-density parity-check codes , Modified variable-length run-length , Hybrid coding architecture , Deoxyribonucleic acid-based data storage , Asymmetric errors , Constrained DNA data storage , Memory , Encoding , Sequential analysis , Decoding , Data storage systems , DNA data storage , Asymmetric substitutions , Constrained codes , DNA sequencing

Citation

Deng, L., Wang, Y., Noor-A-Rahim, M., Guan, Y. L., Shi, Z., Gunawan, E. and Poh, C. L. (2019) 'Optimized Code Design for Constrained DNA Data Storage With Asymmetric Errors', IEEE Access, 7, pp. 84107-84121. (14pp.) DOI: 10.1109/ACCESS.2019.2924827