NOREC4DNA: using near-optimal rateless erasure codes for DNA storage

• Published in: BMC bioinformatics Vol. 22; no. 1; pp. 1 - 406
• Main Authors: Schwarz, Peter Michael, Freisleben, Bernd
• Format: Journal Article
• Language: English
• Published: London BioMed Central 17-08-2021; BMC
• Subjects: Computer programs; Data storage; Deoxyribonucleic acid; Digital data; DNA; DNA biosynthesis; DNA sequencing; DNA storage; Erasure code; Error correction; LT code; Near-optimal rateless erasure code; Nucleotide sequence; Online code; Probability; Raptor code; Software; Storage systems; System effectiveness
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-021-04318-x

Background DNA is a promising storage medium for high-density long-term digital data storage. Since DNA synthesis and sequencing are still relatively expensive tasks, the coding methods used to store digital data in DNA should correct errors and avoid unstable or error-prone DNA sequences. Near-optimal rateless erasure codes, also called fountain codes, are particularly interesting codes to realize high-capacity and low-error DNA storage systems, as shown by Erlich and Zielinski in their approach based on the Luby transform (LT) code. Since LT is the most basic fountain code, there is a large untapped potential for improvement in using near-optimal erasure codes for DNA storage. Results We present NOREC4DNA, a software framework to use, test, compare, and improve near-optimal rateless erasure codes (NORECs) for DNA storage systems. These codes can effectively be used to store digital information in DNA and cope with the restrictions of the DNA medium. Additionally, they can adapt to possible variable lengths of DNA strands and have nearly zero overhead. We describe the design and implementation of NOREC4DNA. Furthermore, we present experimental results demonstrating that NOREC4DNA can flexibly be used to evaluate the use of NORECs in DNA storage systems. In particular, we show that NORECs that apparently have not yet been used for DNA storage, such as Raptor and Online codes, can achieve significant improvements over LT codes that were used in previous work. NOREC4DNA is available on https://github.com/umr-ds/NOREC4DNA. Conclusion NOREC4DNA is a flexible and extensible software framework for using, evaluating, and comparing NORECs for DNA storage systems.