With the amount of data being generated every year increasing exponentially, figuring out where and how to store it efficiently and inexpensively is becoming a larger problem every day. The rapid improvement in performance and cost of DNA synthesis and sequencing methods has led to an increased interest in the use of DNA as a durable and compact medium for data storage. Today, we have a large spectrum of available chemical tools that enable efficient data access and manipulation of in-DNA data. While several DNA storage architectures have been proposed, there is no open-source codec or simulator that implements all of the required components of the DNA-based data storage pipeline for research and development. We present an open-source end-to-end DNA data storage toolkit that can take an input file through the entire DNA storage pipeline. Our work contains implementations of the state-of-the-art techniques for each step of the pipeline, including our own algorithms for each step. These steps include encoding data into DNA strands, simulating the wetlab processes of synthesis, storage and sequencing of those DNA strands, clustering of the sequenced results, reconstruction of DNA strands from noisy clusters, and decoding the initially encoded file with support for error-correction mechanisms. Each module can be used individually or combined to form an entire pipeline. We hope that our toolkit will be useful to researchers and developers who seek to experiment with the new and promising storage technology.

We propose a novel and flexible DNA-storage architecture, which divides the storage space into fixed-size units (blocks) that can be independently and efficiently accessed at random for both read and write operations, and further allows efficient sequential access to consecutive data blocks. In contrast to prior work, in our architecture a pair of random-access PCR primers of length 20 does not define a single object, but an independent storage partition, which is internally blocked and managed independently of other partitions. We expose the flexibility and constraints with which the internal address space of each partition can be managed, and incorporate them into our design to provide rich and functional storage semantics, such as block-storage organization, efficient implementation of data updates, and sequential access. To leverage the full power of the prefix-based nature of PCR addressing, we define a methodology for transforming the internal addressing scheme of a partition into an equivalent that is PCR-compatible. This allows us to run PCR with primers that can be variably elongated to include a desired part of the internal address, and thus narrow down the scope of the reaction to retrieve a specific block or a range of blocks within the partition with sufficiently high accuracy. Our wetlab evaluation demonstrates the practicality of the proposed ideas and a 140x reduction in sequencing cost and latency for retrieval of individual blocks within the partition.

DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the prohibitive cost of reads and writes, the high frequency and the peculiar nature of errors occurring in DNA storage pose a significant challenge to its adoption.