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

doi:10.1109/TNB.2023.3284406

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

2024-01-01

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DOI：10.1109/TNB.2023.3284406

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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% similar to 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.

Keywords:

DNA storage

FASTQ file

fountain code

iterative decoding

luby transform code

oligo

quality score

soft decoding

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

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