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

Abstract

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.

DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage

“…We constrained the encoder output not to include homopolymers longer than three bp to be consistent for all codes to the fixed homopolymer length of the Grass code. We also used the common constraints of a GC content between 40 and 60% 6 , 7 , 21 , 22 in 10 bp intervals for all codes that support it. As an additional constraint for DNA-Aeon, it had to have the lowest total number of encoded bases of all codes evaluated.…”

“…6 ), i.e., our encoder uses principles of arithmetic decoding. The outer code uses the Raptor fountain code implementation of NOREC4DNA 7 in the binary mode, which can generate all possible packets in a given seed range. Users can define either the number of packets generated from a file or the size of the individual packets generated.…”

“…While the code described here is functional on its own, we concatenated it with the NOREC4DNA implementation of a Raptor fountain code 7 as an outer code. Since fountain codes can generate numerous (depending on the implementation, up to infinite) packets from the input data, users can freely adjust the rate of the outer code depending on the anticipated error probabilities, the intended purpose, and the budget.…”

“…DNA as a data storage medium is a promising alternative to traditional storage media for long-term data storage, thanks to its high information density and long life expectancy 4 . During the last years, tremendous progress has been made in the field of DNA data storage research 2 , 5 – 7 . To store digital data in DNA, it first has to be prepared in silico: the binary information is mapped to the four DNA nucleotides (nt) Adenine (A), Guanine (G), Cytosine (C), and Thymine (T).…”

“…Furthermore, we exploit the redundancy introduced into the sequences for constraint adherence to correct insertions, deletions, and substitutions using a sequential decoding algorithm. Finally, we concatenate our code with NOREC4DNA 7 , a Raptor fountain code 20 implementation, using the quality information of the sequential decoding process as an additional input. The fountain code uses this quality information to choose the packets used for the decoding process.…”