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Realtime analysis and visualization of MinION sequencing data with npReader
Minh Duc Cao1, Devika Ganesamoorthy1, Matthew A Cooper1
1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia and.
Bioinformatics (Oxford, England)
|November 12, 2015
Summary
npReader is a new open-source software enabling real-time analysis of Oxford Nanopore MinION sequencing data. This tool facilitates immediate data processing for time-critical applications, unlocking the full potential of nanopore sequencing.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- The Oxford Nanopore MinION platform offers real-time sequencing capabilities.
- Existing software often lacks support for streaming and real-time analysis of MinION data.
- Time-critical applications require immediate data processing during sequencing.
Purpose of the Study:
- To develop an open-source software package for real-time analysis of MinION sequencing data.
- To enable simultaneous extraction and streaming of sequence reads during sequencing.
- To facilitate integration into existing bioinformatics workflows and support development of new streaming algorithms.
Main Methods:
- Developed npReader, an open-source Java-based software package.
- Implemented a command-line interface for workflow integration.
- Created a graphical user interface for real-time run statistics visualization.
- Provided an application programming interface for streaming algorithm development.
Main Results:
- npReader facilitates real-time analysis of MinION sequencing data.
- The software streams sequence reads to downstream pipelines during sequencing.
- It offers both command-line and graphical user interfaces.
- An API is available for advanced streaming algorithm development.
Conclusions:
- npReader addresses the need for real-time analysis tools for MinION data.
- The software enhances the utility of nanopore sequencing for time-sensitive applications.
- npReader is freely available, promoting accessibility and further development in the field.
