Related papers: Coded Shotgun Sequencing
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
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…
A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…
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 tradeoffs of DNA-based storage systems under a simple model, motivated by current…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. The common…
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…
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and…
Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…
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…