Related papers: CRANE: Correcting Errors in Raw Nanopore Signals U…
Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to millions of bases in a single read), and the option to…
The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…
Nanopore sequencers generate raw electrical signals representing the contents of a biological sequence molecule passing through the nanopore. These signals can be analyzed directly, avoiding basecalling entirely. We observe that while…
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…
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…
Recent advancements in nanopore sequencing technology, particularly the R10 nanopore from Oxford Nanopore Technology, have necessitated the development of improved data processing methods to utilize their potential for more than 9-mer…
Nanopore sequencers generate electrical raw signals in real-time while sequencing long genomic strands. These raw signals can be analyzed as they are generated, providing an opportunity for real-time genome analysis. An important feature of…
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…
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…
Summary: Raw nanopore signals can be analyzed while they are being generated, a process known as real-time analysis. Real-time analysis of raw signals is essential to utilize the unique features that nanopore sequencing provides, enabling…
Motivation: Detection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate…
Detecting chemical modifications on RNA molecules remains a key challenge in epitranscriptomics. Traditional reverse transcription-based sequencing methods introduce enzyme- and sequence-dependent biases and fragment RNA molecules,…
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…
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…
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals…
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…
Code agents must both reason over long-horizon repository state and obey strict tool-use protocols. In paired Instruct/Thinking checkpoints, these capabilities are complementary but misaligned. The Instruct model is concise and…
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps…
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…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…