Related papers: Error-Correcting Codes for Nanopore Sequencing
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…
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…
Nanopore sequencing is a promising technology for DNA sequencing. In this paper, we investigate a specific model of the nanopore sequencer, which takes a $q$-ary sequence of length $n$ as input and outputs a vector of length $n+\ell-1$…
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…
The problem of designing codes for deletion-correction and synchronization has received renewed interest due to applications in DNA-based data storage systems that use nanopore sequencers as readout platforms. In almost all instances,…
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…
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 $2t\log_q n+\Theta(\log\log n)$…
Motivated by DNA-based data storage, we investigate a system where digital information is stored in an unordered set of several vectors over a finite alphabet. Each vector begins with a unique index that represents its position in the whole…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
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…
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,…
Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
DNA storage has emerged as a promising solution for large-scale and long-term data preservation. Among various error types, insertions are the most frequent errors occurring in DNA sequences, where the inserted symbol is often identical or…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…