Related papers: SynDe: Syndrome-guided Decoding of Raw Nanopore Re…
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…
Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
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…
As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological…
DNA data storage is rapidly emerging as a promising solution for long-term data archiving, largely due to its exceptional durability. However, the synthesis of DNA strands remains a significant bottleneck in terms of cost and speed. To…
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…
Synchronization errors, such as insertions and deletions, present a fundamental challenge in DNA-based data storage systems, arising from both synthesis and sequencing noise. These channels are often modeled as…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…
The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…
Owing to its several merits over other DNA sequencing technologies, nanopore sequencers hold an immense potential to revolutionize the efficiency of DNA storage systems. However, their higher error rates necessitate further research to…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high…
Barcodes are ubiquitous and have been used in most of critical daily activities for decades. However, most of traditional decoders require well-founded barcode under a relatively standard condition. While wilder conditioned barcodes such as…
This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the…
Splice sites play a crucial role in gene expression, and accurate prediction of these sites in DNA sequences is essential for diagnosing and treating genetic disorders. We address the challenge of splice site prediction by introducing…
Quantum error correction, which utilizes logical qubits that are encoded as redundant multiple physical qubits to find and correct errors in physical qubits, is indispensable for practical quantum computing. Surface code is considered to be…
High-throughput solid-state nanopore experiments generate continuous MHz-rate data streams in which only a small fraction of data contains informative molecular information. This creates storage and processing bottlenecks that limit…