Improved read/write cost tradeoff in DNA-based data storage using LDPC codes
Open accessAbstract
With the amount of data being stored increasing rapidly, there is significant interest in exploring alternative storage technologies. In this context, DNA-based storage systems can offer significantly higher storage densities (petabytes/gram) and durability (thousands of years) than current technologies. Specifically, DNA has been found to be stable over extended periods of time which has been demonstrated in the analysis of organisms long since extinct. Recent advances in DNA sequencing and synthesis pipelines have made DNA-based storage a promising candidate for the storage technology of the future.Recently, there have been multiple efforts in this direction, focusing on aspects such as error correction for synthesis/sequencing errors and erasure correction for handling missing sequences. The typical approach is to use separate codes for handling errors and erasures, but there is limited understanding of the efficiency of this framework. Furthermore, the existing techniques use short block-length codes and heavily rely on read consensus, both of which are known to be suboptimal in coding theory.In this work, we study the tradeoff between the writing and reading costs involved in DNA-based storage and propose a practical scheme to achieve an improved tradeoff between these quantities. Our scheme breaks with the traditional separation framework and instead uses a single large block-length LDPC code for both erasure and error correction. We also introduce novel techniques to handle insertion and deletion errors introduced by the synthesis process. For a range of writing costs, the proposed scheme achieves 30-40% lower reading costs than state-of-the-art techniques on experimental data obtained using array synthesis and Illumina sequencing.The code, data, and Supplementary Material is available at https://github.com/shubhamchandak94/LDPC_ DNA_storage.
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Reed-Solomon code, Fountain codes, and LDPC code were used as an outer code.
“A Reed–Solomon code,4,44,70 Fountain codes,14 and LDPC (low-density parity check) code were used as an outer code.91”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [91]
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D2Sim: A Computational Simulator for Nanopore Sequencing Based DNA Data Storage
Sankar, S., Yixin, W., Noor‐A‐Rahim, M., Gunawan, E., Guan, Y. L., & Poh, C. L. (2026) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbbio.2026.3716589
Sentry-Weave Interleaved Code for Track Hopper-Based DNA Molecular Communication
Yu, Q., Sun, Y., Fu, J., Wang, Q., He, P., & Chen, Y. (2025) · ACM International Conference on Nanoscale Computing and Communication (NANOCOM) · doi:10.1145/3760544.3764136
Error characterization and error correction approaches in combinatorial DNA-based storage
Preuss, I., Sabary, O., Gabrys, R., Zohar Yakhini, B., Yaakobi, E., & Anavy, L. (2026) · Scientific Reports · doi:10.1038/s41598-026-38599-0
DNA-MGC+: A versatile codec for reliable and resource-efficient data storage on synthetic DNAPreprint
Khabbaz, R., Mateos, J., Antonini, M., & Hanna, S. K. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.11.711016
DNA data storage algorithms and synchronization
Hamoum, B. (2022) · theses.fr (ABES) · doi:10.70675/7722069cz1034z4e64z8238z6126d6f7f792
Pandithurai, O., Praveenkumar, J., & Meena Nanditha, S. (2026) · International Conference on System, Computation, Automation and Networking (ICSCAN) · doi:10.1109/icscan66520.2026.11588403
Coverage Depth Analysis: Random Access for DNA Storage over Noisy Channels
Abraham, H., Feldman, I., & Yaakobi, E. (2026) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit62367.2026.11653660
A Sequential Random Sampling Approach to PIR in DNA-based Data Storage
Wang, C., Yaakobi, E., & Zohar Yakhini, B. (2026) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit62367.2026.11654042
DupLeTh: DNA Depolama Sistemlerinde LT Kodları Kullanıldığında Kısmi Kapsama Derinliği Problemi
Akkaya, N., & Haytaoğlu, E. (2026) · Osmaniye Korkut Ata Üniversitesi Fen Bilimleri Enstitüsü Dergisi · doi:10.47495/okufbed.1872317
- Authors
- Chandak, S., Tatwawadi, K., Lau, B., Mardia, J., Kubit, M., Neu, J., Griffin, P., Wootters, M., Weissman, T., & Ji, H.
- Affiliations
- Stanford University (US)
- Corresponding author
- Chandak, Shubham
- ORCID
- Venue
- 2019 57th Annual Allerton Conference on Communication, Control, and Computing (Allerton)
- Publisher
- IEEE
- Published
- 2019-09
- Pages
- 147-156
- OpenAlex
- W2993276217
- Semantic Scholar
- 33fc8fe30dd1a59e6abbe6919ca4fe70d31fdb12
- Cited by
- 80
- References
- 32
- Citations by year
- 2026: 10 · 2025: 9 · 2024: 16 · 2023: 14 · 2022: 12 · 2021: 10 · 2020: 7 · 2019: 2
- FWCI
- 21.55
- Type
- conference paper
- Language
- en
- Open access
- green
- doi.org
- Locations
- Allerton Conference on Communication, Control, and Computing (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- Funders
- National Science Foundation (1807371)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Physical Sciences › Computer Science › Computer Networks and Communications › Error Correcting Code Techniques
- Physical Sciences › Computer Science › Computer Networks and Communications › Advanced Data Storage Technologies
- Keywords
- DNA data storage, LDPC codes, erasure correction, error correction, insertion and deletion errors, DNA sequencing errors
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