20 papers · ranked by Valyu relevance
Matei David, L J Dursi, Delia Yao, Paul C Boutros + 2 more
The MinION produced by Oxford Nanopore Technologies (ONT) is a highly portable, third-generation sequencing instrument, comparable in size to a cell phone. The small form factor makes the MinION particularly suitable for sequencing experiments performed in remote locations (). However, the MinION relies on the cloud…
Xuan Lv, Zhiguang Chen, Yutong Lu, Yuedong Yang
Oxford Nanopore sequencing is fastly becoming an active field in genomics, and it’s critical to basecall nucleotide sequences from the complex electrical signals. Many efforts have been devoted to developing new basecalling tools over the years. However, the basecalled reads still suffer from a high error rate and slow…
Marc Pagès-Gallego, Jeroen de Ridder
Background Nanopore-based DNA sequencing relies on basecalling the electric current signal. Basecalling requires neural networks to achieve competitive accuracies. To improve sequencing accuracy further, new models are continuously proposed with new architectures. However, benchmarking is currently not standardized…
Adam Napieralski, Robert Nowak, Maria Gabriella Xibilia
Third-generation DNA sequencers provided by Oxford Nanopore Technologies (ONT) produce a series of samples of an electrical current in the nanopore. Such a time series is used to detect the sequence of nucleotides. The task of translation of current values into nucleotide symbols is called basecalling. Various…
Gagandeep Singh, Mohammed Alser, Kristof Denolf, Can Firtina + 4 more
Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The performance of basecalling has critical implications for all later steps in genome analysis. Therefore, there is a need to reduce the…
Matei David, L.J. Dursi, Delia Yao, Paul C. Boutros + 1 more
The highly portable Oxford Nanopore MinlON sequencer has enabled new applications of genome sequencing directly in the field. However, the MinlON currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated sequencing data into basecalls. To allow offline and private…
Gagandeep Singh, Mohammed Alser, Kristof Denolf, Can Firtina + 4 more
'Alireza Khodamoradi' 'Meryem Banu Cavlak' 'Henk Corporaal' 'Onur Mutlu'] Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The performance of basecalling has critical implications for all later…
Ryan R. Wick, Louise M. Judd, Kathryn E. Holt
Basecalling, the computational process of translating raw electrical signal to nucleotide sequence, is of critical importance to the sequencing platforms produced by Oxford Nanopore Technologies (ONT). Here we examine the performance of different basecalling tools, looking at accuracy at the level of bases within…
Zhongxu Zhu
Nanopore sequencing, a third-generation sequencing technique, enables direct RNA sequencing, real-time analysis, and long-read length. Nanopore sequencers measure electrical current changes as nucleotides pass through nanopores; a basecaller identifies base sequences according to the raw current measurements. However…
Scott Ferguson, Todd McLay, Rose L. Andrew, Jeremy J. Bruhl + 3 more
'Benjamin Schwessinger' 'Justin Borevitz' 'Ashley Jones'] Background Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is basecalling, the…
Gagandeep Singh, Mohammed Alser, Alireza Khodamoradi, Kristof Denolf + 4 more
'Can Fırtına' 'Meryem Banu Cavlak' 'Henk Corporaal' 'Onur Mutlu'] Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The performance of basecalling has critical implications for all later steps in…
Xuechun Xu, Joakim Jaldén
—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 resolution fully. The processing of the ion currents predominantly utilizes neural…
Neven Miculinić, Marko Ratković, Mile Šikić
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 present MinCall, an end2end basecaller model for the MinION. The model is based…
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Fırtına + 5 more
'Joël Lindegger' 'Mohammad Sadrosadati' 'Nika Mansouri Ghiasi' 'Can Alkan' 'Onur Mutlu'] Basecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art basecallers employ complex deep learning models to…
Marc Pagès-Gallego, Jeroen de Ridder
Nanopore basecalling is a difficult task which requires the use of complex algorithms and neural network models to achieve competitive accuracies. These algorithms, called basecallers, are developed continuously both by ONT and the scientific community in an effort to improve basecalling accuracies. With the rapidly…
Parv Agarwal, Thomas Heinis
DNA data storage is rapidly gaining traction as a long-term data archival solution, primarily due to its exceptional durability. Retrieving stored data relies on DNA sequencing, which involves a process called basecalling — a typically costly and slow task that uses machine learning to map raw sequencing signals back…
Jasmine Quah, Omer Sella, Thomas Heinis
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring DNA in the life sciences. To achieve higher accuracy for previously unseen…
Ziyuan Wang, Ziyang Liu, Yinshan Fang, Hao Helen Zhang + 4 more
Accurately basecalling sequence backbones in the presence of nucleotide modifications remains a substantial challenge in nanopore sequencing bioinformatics. It has been extensively demonstrated that state-of-the-art basecallers are less compatible with modification-induced sequencing signals. A precise basecalling, on…
Zhichu Ren, Zhen Zhang, Yunsheng Tian, Ju Li
Autonomous laboratories were previously controlled mainly by scripting languages such as Python, limiting their usage among experimentalists. The recent release of OpenAI's ChatGPT API's function calling feature has enabled seamless integration and execution of Python subroutines in experimental workflows using voice…
Zhichu Ren, Zhen Zhang, Yunsheng Tian, Ju Li
Autonomous laboratories were previously controlled mainly by scripting languages such as Python, limiting their usage among experimentalists. The recent release of OpenAI's ChatGPT API's function calling feature has enabled seamless integration and execution of Python subroutines in experimental workflows using voice…