Cooperative sequence clustering and decoding for DNA storage system with fountain codes

Jaeho Jeong, Seong-Joon Park, Jae-Won Kim, Jong-Seon No, Ha Hyeon Jeon, Jeong Wook Lee, Albert No, Sunghwan Kim, Hosung Park

Abstract: In DNA storage systems, there are tradeoffs between writing and reading costs. Increasing the code rate of error-correcting codes may save writing cost, but it will need more sequence reads for data retrieval. There is potentially a way to improve sequencing and decoding processes in such a way that the reading cost induced by this tradeoff is reduced without increasing the writing cost. In past researches, clustering, alignment and decoding processes were considered as separate stages but we believe that using the information from all these processes together may improve decoding performance. Actual experiments of DNA synthesis and sequencing should be performed because simulations cannot be relied on to cover all error possibilities in practical circumstances.