CMOSS: A Reliable, Motif-based Columnar Molecular Storage System

TL;DR

CMOSS is a novel DNA storage system that uses a motif-based vertical layout and fixed-size blocks to improve error tolerance, reduce costs, and enable efficient random access, validated through simulations and experiments.

Contribution

It introduces a new motif-based vertical layout and fixed-size block organization for DNA storage, enhancing error correction and access efficiency over state-of-the-art methods.

Findings

CMOSS achieves lower read/write costs compared to existing systems.

The vertical layout enables merged consensus calling and decoding.

Experimental results validate the robustness and efficiency of CMOSS.

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.