Related papers: Low-redundancy codes for correcting multiple short…
Erasure coding techniques are getting integrated in networked distributed storage systems as a way to provide fault-tolerance at the cost of less storage overhead than traditional replication. Redundancy is maintained over time through…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
Synthetic DNA approaches 227.5 exabytes per gram of storage density with stability over millennial timescales. Realising this capacity requires error-correction codes that recover data from substantial synthesis and sequencing errors.…
DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…
In this paper, we construct systematic $q$-ary two-deletion correcting codes and burst-deletion correcting codes, where $q\geq 2$ is an even integer. For two-deletion codes, our construction has redundancy $5\log n+O(\log q\log\log n)$ and…
The problem of correcting deletions and insertions has recently received significantly increased attention due to the DNA-based data storage technology, which suffers from deletions and insertions with extremely high probability. In this…
Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…
Scientific computing workflows generate enormous distributed data that is short-lived, yet critical for job completion time. This class of data is called intermediate data. A common way to achieve high data availability is to replicate…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Owing to its several merits over other DNA sequencing technologies, nanopore sequencers hold an immense potential to revolutionize the efficiency of DNA storage systems. However, their higher error rates necessitate further research to…
We study the combination of two recent coding approaches, in the context of DNA based data storage. Composite DNA alphabets leverage properties of the DNA synthesis and sequencing process. A composite symbol does not represent a single…
Imperfect measurement can degrade a quantum error correction scheme. A solution that restores fault tolerance is to add redundancy to the process of syndrome extraction. In this work, we show how to optimize this process for an arbitrary…
An error-erasure channel is a simple noise model that introduces both errors and erasures. While the two types of errors can be corrected simultaneously with error-correcting codes, it is also known that any linear code allows for first…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…
Erasure coding is a storage-efficient alternative to replication for achieving reliable data backup in distributed storage systems. During the storage process, traditional erasure codes require a unique source node to create and upload all…
In this paper, for any fixed positive integers $t$ and $q>2$, we construct $q$-ary codes correcting a burst of at most $t$ deletions with redundancy $\log n+8\log\log n+o(\log\log n)+\gamma_{q,t}$ bits and near-linear encoding/decoding…
The main obstacles for the practical deployment of DNA-based data storage platforms are the prohibitively high cost of synthetic DNA and the large number of errors introduced during synthesis. In particular, synthetic DNA products contain…