Related papers: Using Sequence Ensembles for Seeding Alignments of…
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we…
The Oxford Nanopore Technologies's MinION is the first portable DNA sequencing device. It is capable of producing long reads, over 100 kBp were reported. However, it has significantly higher error rate than other methods. In this study, we…
Despite their significant advantages over competing technologies, nanopore sequencers are plagued by high error rates, due to physical characteristics of the nanopore and inherent noise in the biological processes. It is thus paramount not…
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…
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…
We investigate usage of dynamic time warping (DTW) algorithm for aligning raw signal data from MinION sequencer. DTW is mostly using for fast alignment for selective sequencing to quickly determine whether a read comes from sequence of…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA…
Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the…
The MinION is a recent-to-market handheld nanopore sequencer. It can be used to determine the whole genome of a target virus in a biological sample. Its Read Until feature allows us to skip sequencing a majority of non-target reads (DNA/RNA…
Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long…
In nanopore sequencing, electrical signal is measured as DNA molecules pass through the sequencing pores. Translating these signals into DNA bases (base calling) is a highly non-trivial task, and its quality has a large impact on the…
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…
Running machine learning inference on tiny devices, known as TinyML, is an emerging research area. This task requires generating inference code that uses memory frugally, a task that standard ML frameworks are ill-suited for. A deployment…
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 minimizers sampling mechanism is a popular mechanism for string sampling introduced independently by Schleimer et al. [SIGMOD 2003] and by Roberts et al. [Bioinf. 2004]. Given two positive integers $w$ and $k$, it selects the…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
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…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Randomised algorithms often employ methods that can fail and that are retried with independent randomness until they succeed. Randomised data structures therefore often store indices of successful attempts, called seeds. If $n$ such seeds…