R&D: Mainstream Encoding–Decoding Methods of DNA Storage

CCF Transactions on High Performance Computing has published an article written by Chenyang Wang, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China, and University of Chinese Academy of Sciences, Beijing, China, Guannan Ma, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China, Di Wei, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China, Xinru Zhang, Key Lab of Intelligent Information Processing, State Key Lab of Computer Architecture, Big-data Academy, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China, and University of Chinese Academy of Sciences, Beijing, China, Peihan Wang, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China, and University of Chinese Academy of Sciences, Beijing, China, Cuidan Li, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China, Jing Xing, Key Lab of Intelligent Information Processing, State Key Lab of Computer Architecture, Big-data Academy, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China, Zheng Wei, Key Lab of Intelligent Information Processing, State Key Lab of Computer Architecture, Big-data Academy, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China, Bo Duan, Western Institute of Computing Technology, Chongqing, China, Dongxin Yang, Pei Wang, Western Institute of Computing Technology, Chongqing, China, Dongbo Bu, Key Lab of Intelligent Information Processing, State Key Lab of Computer Architecture, Big-data Academy, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China, and University of Chinese Academy of Sciences, Beijing, China, and Fei Chen, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China, and University of Chinese Academy of Sciences, Beijing, China.

Abstract: “DNA storage is a new digital data storage technology based on specific encoding and decoding methods between 0 and 1 binary codes of digital data and A-T-C-G quaternary codes of DNAs, which and is expected to develop into a major data storage form in the future due to its advantages (such as high data density, long storage time, low energy consumption, convenience for carrying, concealed transportation and multiple encryptions). In this review, we mainly summarize the recent research advances of four main encoding and decoding methods of DNA storage technology: direct mapping method between 0 and 1 binary and A-T-C-G quaternary codes in early-stage, fountain code for higher logical storage density, inner and outer codes for random access DNA storage data, and CRISPR mediated in vivo DNA storage method. The first three encoding/decoding methods belong to in vitro DNA storage, representing the mainstream research and application in DNA storage. Their advantages and disadvantages are also reviewed: direct mapping method is easy and efficient, but has high error rate and low logical density; fountain code can achieve higher storage density without random access; inner and outer code has error-correction design to realize random access at the expense of logic density. This review provides important references and improved understanding of DNA storage methods. Development of efficient and accurate DNA storage encoding and decoding methods will play a very important and even decisive role in the transition of DNA storage from the laboratory to practical application, which may fundamentally change the information industry in the future.“