1. High capacity DNA data storage with variable-length Oligonucleotides using repeat accumulate code and hybrid mapping
- Author
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Jingyun Zhang, Yixin Wang, Noor-A-Rahim, Erry Gunawan, Chueh Loo Poh, Yong Liang Guan, and School of Electrical and Electronic Engineering
- Subjects
0301 basic medicine ,Environmental Engineering ,Computer science ,DNA digital data storage ,Repeat-accumulate code ,Digital data ,Biomedical Engineering ,Long Term Data Storage ,02 engineering and technology ,Data loss ,03 medical and health sciences ,0202 electrical engineering, electronic engineering, information engineering ,Molecular Biology ,lcsh:QH301-705.5 ,business.industry ,Oligonucleotide ,Research ,020206 networking & telecommunications ,Next-generation information storage ,Cell Biology ,DNA Data Storage ,DNA data storage ,Long term data storage ,030104 developmental biology ,lcsh:Biology (General) ,Computer data storage ,Electrical and electronic engineering [Engineering] ,business ,Error detection and correction ,Algorithm ,Coding (social sciences) - Abstract
Background With the inherent high density and durable preservation, DNA has been recently recognized as a distinguished medium to store enormous data over millennia. To overcome the limitations existing in a recently reported high-capacity DNA data storage while achieving a competitive information capacity, we are inspired to explore a new coding system that facilitates the practical implementation of DNA data storage with high capacity. Result In this work, we devised and implemented a DNA data storage scheme with variable-length oligonucleotides (oligos), where a hybrid DNA mapping scheme that converts digital data to DNA records is introduced. The encoded DNA oligos stores 1.98 bits per nucleotide (bits/nt) on average (approaching the upper bound of 2 bits/nt), while conforming to the biochemical constraints. Beyond that, an oligo-level repeat-accumulate coding scheme is employed for addressing data loss and corruption in the biochemical processes. With a wet-lab experiment, an error-free retrieval of 379.1 KB data with a minimum coverage of 10x is achieved, validating the error resilience of the proposed coding scheme. Along with that, the theoretical analysis shows that the proposed scheme exhibits a net information density (user bits per nucleotide) of 1.67 bits/nt while achieving 91% of the information capacity. Conclusion To advance towards practical implementations of DNA storage, we proposed and tested a DNA data storage system enabling high potential mapping (bits to nucleotide conversion) scheme and low redundancy but highly efficient error correction code design. The advancement reported would move us closer to achieving a practical high-capacity DNA data storage system.
- Published
- 2019
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