  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.
