Related papers: Correcting Contextual Deletions in DNA Nanopore Re…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that…
Despite their significant advantages over competing technologies, nanopore sequencers are plagued by high error rates, due to physical characteristics of the nanopore and inherent noise in the biological processes. It is thus paramount not…
We consider the problem of designing low-redundancy codes in settings where one must correct deletions in conjunction with substitutions or adjacent transpositions; a combination of errors that is usually observed in DNA-based data storage.…
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 deletion-correcting codes for an adversarial nanopore channel in which at most $t$ deletions may occur. We propose an explicit construction of $q$-ary codes of length $n$ for this channel with $2t\log_q n+\Theta(\log\log n)$…
In coding theory, handling errors that occur when symbols are inserted or deleted from a transmitted message is a long-standing challenge. Optimising redundancy for insertion and deletion channels remains a key open problem with significant…
One of the main challenges in developing racetrack memory systems is the limited precision in controlling the track shifts, that in turn affects the reliability of reading and writing the data. A current proposal for combating deletions in…
We consider the problem of constructing codes that can correct deletions that are localized within a certain part of the codeword that is unknown a priori. Namely, the model that we study is when at most $k$ deletions occur in a window of…
We study codes that can correct backtracking errors during nanopore sequencing. In this channel, a sequence of length $n$ over an alphabet of size $q$ is being read by a sliding window of length $\ell$, where from each window we obtain only…
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…
Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions,…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic…
In this paper, we investigate the optimum way to allocate redundancy of finite-length nested codes for modern nonvolatile memories suffering from both permanent defects and transient errors (erasures or random errors). A nested coding…
This paper studies codes that correct bursts of deletions. Namely, a code will be called a $b$-burst-deletion-correcting code if it can correct a deletion of any $b$ consecutive bits. While the lower bound on the redundancy of such codes…
In this paper, we present an efficiently encodable and decodable code construction that is capable of correction a burst of deletions of length at most $k$. The redundancy of this code is $\log n + k(k+1)/2\log \log n+c_k$ for some constant…
Motivated by average-case trace reconstruction and coding for portable DNA-based storage systems, we initiate the study of \emph{coded trace reconstruction}, the design and analysis of high-rate efficiently encodable codes that can be…
Consider two or more strings $\mathbf{x}^1,\mathbf{x}^2,\ldots,$ that are concatenated to form $\mathbf{x}=\langle \mathbf{x}^1,\mathbf{x}^2,\ldots \rangle$. Suppose that up to $\delta$ deletions occur in each of the concatenated strings.…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…