The surge in demand for cost-effective 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 in DNA poses several challenges as the technology used for reading/writing data on DNA are highly error prone. Thus, it is important to design pipelines that can efficiently use redundancy to mask errors without amplifying read/write 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 state-of-the-art (SOTA) on three fronts (i) a motif-based, vertical layout in contrast to nucleotide-based horizontal layout, (ii) integrated consensus calling and decoding enabled by the vertical layout, and (iii) a flexible, block-based data organization for random access over DNA storage in contrast to object-based organization. Using an in-depth evaluation with several simulated and real wet lab experiments, we demonstrate the benefits of CMOSS design.

Given the growing adoption of AI, cloud data lakes are facing the need to support cost-effective "just-in-case" data archival over long time periods to meet regulatory compliance requirements. Unfortunately, current media technologies suffer from fundamental issues that will soon, if not already, make cost-effective data archival infeasible. In this paper, we present a vision for redesigning the archival tier of cloud data lakes based on a novel, obsolescence-free storage medium-synthetic DNA. In doing so, we make two contributions: (i) we highlight the challenges in using DNA for data archival and list several open research problems, (ii) we outline OligoArchive-DSM (OA-DSM)-an end-to-end DNA storage pipeline that we are developing to demonstrate the feasibility of our vision.

Synthetic DNA has received much attention recently as a long-term archival medium alternative due to its high density and durability characteristics. However, most current work has primarily focused on using DNA as a precise storage medium. In this work, we take an alternate view of DNA. Using neural-network-based compression techniques, we transform images into a latent-space representation, which we then store on DNA. By doing so, we transform DNA into an approximate image storage medium, as images generated back from DNA are only approximate representations of the original images. Using several datasets, we investigate the storage benefits of approximation, and study the impact of DNA storage errors (substitutions, indels, bias) on the quality of approximation. In doing so, we demonstrate the feasibility and potential of viewing DNA as an approximate storage medium.

BACKGROUND: Improvements in sequencing technology continue to drive sequencing cost towards $100 per genome. However, mapping sequenced data to a reference genome remains a computationally-intensive task due to the dependence on edit distance for dealing with INDELs and mismatches introduced by sequencing. All modern aligners use seed-filter-extend methodology and rely on filtration heuristics to reduce the overhead of edit distance computation. However, filtering has inherent performance-accuracy trade-offs that limits its effectiveness. RESULTS: Motivated by algorithmic advances in randomized low-distortion embedding, we introduce SEE, a new methodology for developing sequence mappers and aligners. While SFE focuses on eliminating sub-optimal candidates, SEE focuses instead on identifying optimal candidates. To do so, SEE transforms the read and reference strings from edit distance regime to the Hamming regime by embedding them using a randomized algorithm, and uses Hamming distance over the embedded set to identify optimal candidates. To show that SEE performs well in practice, we present Accel-Align an SEE-based short-read sequence mapper and aligner that is 3-12[Formula: see text] faster than state-of-the-art aligners on commodity CPUs, without any special-purpose hardware, while providing comparable accuracy. CONCLUSIONS: As sequencing technologies continue to increase read length while improving throughput and accuracy, we believe that randomized embeddings open up new avenues for optimization that cannot be achieved by using edit distance. Thus, the techniques presented in this paper have a much broader scope as they can be used for other applications like graph alignment, multiple sequence alignment, and sequence assembly.