Related papers: Improved Coding over Sets for DNA-Based Data Stora…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
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…
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…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
DNA strands serve as a storage medium for $4$-ary data over the alphabet $\{A,T,G,C\}$. DNA data storage promises formidable information density, long-term durability, and ease of replicability. However, information in this intriguing…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs…
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.…
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…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
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…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and trade-offs of DNA-based storage systems by introducing a new channel model, which we…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…