Related papers: Error-Correcting Codes for Nanopore Sequencing
We consider the problem of designing low-redundancy codes in settings where one must correct deletions in conjunction with substitutions or adjacent transpositions; a combination of errors that is usually observed in DNA-based data storage.…
Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that…
Recently, codes for correcting a burst of errors have attracted significant attention. One of the most important reasons is that bursts of errors occur in certain emerging techniques, such as DNA storage. In this paper, we investigate a…
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…
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 propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for…
Nanopore protein sequencing produces long, noisy ionic current traces in which key molecular phases, such as protein capture and translocation, are embedded. Capture phases mark the successful entry of a protein into the pore and serve as…
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…
We present a constraint-coding scheme to correct asymmetric magnitude-$1$ errors in multi-level non-volatile memories. For large numbers of such errors, the scheme is shown to deliver better correction capability compared to known…
Error correction code is a major part of the communication physical layer, ensuring the reliable transfer of data over noisy channels. Recently, neural decoders were shown to outperform classical decoding techniques. However, the existing…
Oxford Nanopore MinION sequencer is currently the smallest sequencing device available. While being able to produce very long reads (reads of up to 100~kbp were reported), it is prone to high sequencing error rates of up to 30%. Since most…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
Repetition code forms a fundamental basis for quantum error correction experiments. To date, it stands as the sole code that has achieved large distances and extremely low error rates. Its applications span the spectrum of evaluating…
Nanopore based sequencing has demonstrated significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multi-layered…
Fast, reliable and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress of various nanopore-based sequencing configurations,…
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…
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…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…
In this paper, for any fixed positive integers $t$ and $q>2$, we construct $q$-ary codes correcting a burst of at most $t$ deletions with redundancy $\log n+8\log\log n+o(\log\log n)+\gamma_{q,t}$ bits and near-linear encoding/decoding…
This paper studies codes that correct bursts of deletions. Namely, a code will be called a $b$-burst-deletion-correcting code if it can correct a deletion of any $b$ consecutive bits. While the lower bound on the redundancy of such codes…