scholarly journals Sequoia: An interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets

2019 ◽  
Author(s):  
Ratanond Koonchanok ◽  
Swapna Vidhur Daulatabad ◽  
Quoseena Mir ◽  
Khairi Reda ◽  
Sarath Chandra Janga
Keyword(s):  
Visual Analytics ◽  
Dynamic Time Warping ◽  
Visualization Tool ◽  
Web Interface ◽  
Time Warping ◽  
Front End ◽  
Oxford Nanopore ◽  
Dynamic Time ◽  
Oxford Nanopore Technologies

AbstractSequoia is a visualization tool that allows biologists to explore characteristics of signals generated by the Oxford Nanopore Technologies (ONT) in detail. From Fast5 files generated by ONT, the tool displays relative similarities between signals using the dynamic time warping and the t-SNE algorithms. Raw signals can be visualized through mouse actions while particular signals of interest can also be exported as a CSV file for further analysis. Sequoia consists of two major components: the command-line back-end that performs necessary computations using Python and the front-end that displays the visualization through a web interface. Two datasets are used to conduct a case study in order to illustrate the usability of the tool.

scholarly journals Real time selective sequencing using nanopore technology.

2016 ◽  
Author(s):  
Matthew Loose ◽  
Sunir Malla ◽  
Michael Stout
Keyword(s):  
Real Time ◽  
Dynamic Time Warping ◽  
Current Flow ◽  
Direct Selection ◽  
Dna Molecules ◽  
Time Warping ◽  
Oxford Nanopore ◽  
Flow Through ◽  
Dynamic Time ◽  
Selection Of

The Oxford Nanopore MinION is a portable real time sequencing device which functions by sensing the change in current flow through a nanopore as DNA passes through it. These current values can be streamed in real time from individual nanopores as DNA molecules traverse them. Furthermore, the technology enables individual DNA molecules to be rejected on demand by reversing the voltage across specific channels. In theory, combining these features enables selection of individual DNA molecules for sequencing from a pool, an approach called "Read Until". Here we apply dynamic time warping to match short query current traces to references, demonstrating selection of specific regions of small genomes, individual amplicons from a group of targets, or normalisation of amplicons in a set. This is the first demonstration of direct selection of specific DNA molecules in real time whilst sequencing on any device and enables many novel uses for the MinION.

Multichannel sparse spike deconvolution based on dynamic time warping

2021 ◽  
Author(s):  
Xiaowei Zhao ◽  
Shangxu Wang ◽  
Sanyi Yuan ◽  
Liang Cheng ◽  
Youjun Cai
Keyword(s):  
Dynamic Time Warping ◽  
Time Warping ◽  
Dynamic Time
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