Abstract

BackgroundDNA 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.ResultsWe 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.ConclusionNOREC4DNA is a flexible and extensible software framework for using, evaluating, and comparing NORECs for DNA storage systems.

Highlights

  • ResultsWe present NOREC4DNA, a software framework to use, test, compare, and improve near-optimal rateless erasure codes (NORECs) for deoxyribonucleic acid (DNA) storage systems

  • deoxyribonucleic acid (DNA) is a promising storage medium for high-density long-term digital data storage

  • We show that near-optimal rateless erasure code (NOREC) belong to the most suitable codes for DNA storage; Raptor codes yield the best results across all tested metrics

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Summary

Results

NOREC4DNA provides several simulators to compare different codes under various aspects. It has to be mentioned that the image as the chosen input file has longer sequences of the same symbols, which results in a corresponding distribution in the generated DNA strand This shows that an implementation of the Raptor code in the form of a systematic code would not have a positive impact on the created packets. By comparing the 1 kb Lorem Ipsum file with the 100 kb version (Configuration 1 and Configuration 9), we see that with an increase from an average of 4.5 s for the 1 kb file and 17.5 seconds for the 100 kb file, the time required for encoding does not significantly increase with the input file size We conducted this experiment with a 1 Mb file containing random ASCII characters using 4 Reed–Solomon symbols per packet. Even for larger files, NOREC4DNA can generate sequences in a timely fashion in the order of seconds or minutes

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