Related papers: Error-Correcting Codes for Nanopore Sequencing
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
Purpose Nanopore-based molecular sensing and measurement, specifically Deoxyribonucleic acid (DNA) sequencing, is advancing at a fast pace. Some embodiments have matured from coarse particle counters to enabling full human genome assembly.…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
In this paper, we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where data is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
In nanopore sequencing, electrical signal is measured as DNA molecules pass through the sequencing pores. Translating these signals into DNA bases (base calling) is a highly non-trivial task, and its quality has a large impact on the…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the…
Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…
Nanopore sequencing is an emerging DNA sequencing technology that has been proposed for use in DNA storage systems. We propose the noisy nanopore channel model for nanopore sequencing. This model captures duplications, inter-symbol…
DNA is an attractive candidate for data storage. Its millennial durability and nanometer scale offer exceptional data density and longevity. Its relevance to medical applications also drives advances in DNA-related biotechnology. To protect…
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
Codes correcting bursts of deletions and localized deletions have garnered significant research interest in recent years. One of the primary objectives is to construct codes with minimal redundancy. Currently, the best known constructions…
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…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
We introduce the sum channel, a new channel model motivated by applications in distributed storage and DNA data storage. In the error-free case, it takes as input an $\ell$-row binary matrix and outputs an $(\ell+1)$-row matrix whose first…
Two-dimensional error-correcting codes, where codewords are represented as $n \times n$ arrays over a $q$-ary alphabet, find important applications in areas such as QR codes, DNA-based storage, and racetrack memories. Among the possible…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes…
Synchronization errors, such as insertions and deletions, present a fundamental challenge in DNA-based data storage systems, arising from both synthesis and sequencing noise. These channels are often modeled as…
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…