CMOSS: A Reliable, Motif-based Columnar Molecular Storage System (2405.17138v1)

Abstract: The surge in demand for cost-effective, durable long-term archival media, coupled with density limitations of contemporary magnetic media, has resulted in synthetic DNA emerging as a promising new alternative. Despite its benefits, storing data on DNA poses several challenges as the technology used for reading/writing data and achieving random access on DNA are highly error prone. In order to deal with such errors, it is important to design efficient pipelines that can carefully use redundancy to mask errors without amplifying overall cost. In this work, we present Columnar MOlecular Storage System (CMOSS), a novel, end-to-end DNA storage pipeline that can provide error-tolerant data storage at low read/write costs. CMOSS differs from SOTA on three fronts (i) a motif-based, vertical layout in contrast to nucleotide-based horizontal layout used by SOTA, (ii) merged consensus calling and decoding enabled by the vertical layout, and (iii) a flexible, fixed-size, block-based data organization for random access over DNA storage in contrast to the variable-sized, object-based access used by SOTA. Using an in-depth evaluation via simulation studies and real wet-lab experiments, we demonstrate the benefits of various CMOSS design choices. We make the entire pipeline together with the read datasets openly available to the community for faithful reproduction and furthering research.