Related papers: Correcting Multiple Substitutions in Nanopore-Sequ…
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to…
In this work, we investigate the problem of constructing codes capable of correcting two deletions. In particular, we construct a code that requires redundancy approximately 8 log n + O(log log n) bits of redundancy, where n is the length…
Recent work by Smagloy et al. (ISIT 2020) shows that the redundancy of a single-deletion $s$-substitution correcting code is asymptotically at least $(s+1)\log n+o(\log n)$, where $n$ is the length of the codes. They also provide a…
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…
We first give a construction of binary $t_1$-deletion-$t_2$-insertion-burst correcting codes with redundancy at most $\log(n)+(t_1-t_2-1)\log\log(n)+O(1)$, where $t_1\ge 2t_2$. Then we give an improved construction of binary codes capable…
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…
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 $2t\log_q n+\Theta(\log\log n)$…
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…
Quantum error correction is expected to be essential in large-scale quantum technologies. However, the substantial overhead of qubits it requires is thought to greatly limit its utility in smaller, near-term devices. Here we introduce a new…
We study segmented burst-deletion channels motivated by the observation that synchronization errors commonly occur in a bursty manner in real-world settings. In this channel model, transmitted sequences are implicitly divided into…
Near term quantum computers suffer from the presence of different noise sources. In order to mitigate for this effect and acquire results with significantly better accuracy, there is the urge of designing efficient error correction or error…
The analysis of the decoding failure rate of the bit-flipping algorithm has received increasing attention. For a binary linear code we consider the minimum number of rows in a parity-check matrix such that the bit-flipping algorithm is able…
Error correction is essential for modern computing systems, enabling information to be processed accurately even in the presence of noise. Here, we demonstrate a new approach which exploits an error correcting phase that emerges in a system…
Motivated by the concept of probe storage, we study the problem of information retrieval using a large array of N nano-mechanical probes, N ~ 4000. At the nanometer scale it is impossible to avoid errors in the positioning of the array,…
In this paper, we consider a recent channel model of a nanopore sequencer proposed by McBain, Viterbo, and Saunderson (2024), termed the noisy nanopore channel (NNC). In essence, an NNC is a duplication channel with structured, Markov…
The scaling of high density NOR Flash memory devices with multi level cell (MLC) hits the reliability break wall because of relatively high intrinsic bit error rate (IBER). The chip maker companies offer two solutions to meet the output bit…
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…
The problem of error correction in both coherent and noncoherent network coding is considered under an adversarial model. For coherent network coding, where knowledge of the network topology and network code is assumed at the source and…
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…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…