相关论文: Error-correcting Codes for Noisy Duplication Chann…
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…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
This paper introduces a new solution to DNA storage that integrates all three steps of retrieval, namely clustering, reconstruction, and error correction. DNA-correcting codes are presented as a unique solution to the problem of ensuring…
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length $k$ is the insertion of the reversed and complemented copy of a substring of length $k$ adjacent to its…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
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…
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…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…
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…
We consider error-correcting coding for DNA-based storage. We model the DNA storage channel as a multi-draw IDS channel where the input data is chunked into $M$ short DNA strands, which are copied a random number of times, and the channel…
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.…
Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…
Synthetic DNA can in principle be used for the archival storage of arbitrary data. Because errors are introduced during DNA synthesis, storage, and sequencing, an error-correcting code (ECC) is necessary for error-free recovery of the data.…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
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…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…