Iterative Soft Decoding Algorithm for DNA Storage Using Quality Score and Redecoding

Ever since deoxyribonucleic acid (DNA) was considered as a next-generation data-storage medium, lots of research efforts have been made to correct errors occurred during the synthesis, storage, and sequencing processes using error correcting codes (ECCs). Previous works on recovering the data from the sequenced DNA pool with errors have utilized hard decoding algorithms based on a majority decision rule. To improve the correction capability of ECCs and robustness of the DNA storage system, we propose a new iterative soft decoding algorithm, where soft information is obtained from FASTQ files and channel statistics. In particular, we propose a new formula for log-likelihood ratio (LLR) calculation using quality scores (Q-scores) and a redecoding method which may be suitable for the error correction and detection in the DNA sequencing area. Based on the widely adopted encoding scheme of the fountain code structure proposed by Erlich et al., we use three different sets of sequenced data to show consistency for the performance evaluation. The proposed soft decoding algorithm gives 2.3% $\sim $ 7.0% improvement of the reading number reduction compared to the state-of-the-art decoding method and it is shown that it can deal with erroneous sequenced oligo reads with insertion and deletion errors.

I. Introduction

As huge amounts of data are rapidly produced in the era of big data, there is a need for a new type of high-density storage media that is more competitive than existing ones such as magnetic tapes or hard disk drives. Major information technology companies are spending enormous financial resources for building new data centers to cope with the increased storage demand. With the development of new synthesis and sequencing technologies, deoxyribonucleic acid (DNA) has been considered as a competitive candidate for new storage media [1]. DNA is known to have up to more than hundreds of million times information density compared to the existing storage media and can survive thousands of years when the temperature is kept appropriately [2]. Since the pioneering study in [1], the idea of using DNA as a storage medium has attracted a significant attention and a lot of studies are going on to make use of the advantages of its longevity and high information density nowadays.