Related papers: Modular non-repeating codes for DNA storage
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
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…
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 describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
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.…
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…
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…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
This work presents a theoretical analysis of the probability of successfully retrieving data encoded with MDS codes (e.g., Reed-Solomon codes) in DNA storage systems. We study this probability under independent and identically distributed…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
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…
A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…
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…
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,…
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 applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
In modern age, the increasing complexity of computation and communication technology is leading us towards the necessity of new paradigm. As a result, unconventional approach like DNA coding theory is gaining considerable attention. The…