Award details

poRe: visualization and analysis of nanopore sequencing data for rapid and mobile pathogen detection

Reference	BB/M020037/1
Principal Investigator / Supervisor	Professor Michael Watson
Co-Investigators / Co-Supervisors
Institution	University of Edinburgh
Department	The Roslin Institute
Funding type	Research
Value (£)	148,651
Status	Completed
Type	Research Grant
Start date	01/07/2015
End date	31/12/2016
Duration	18 months

Abstract

Nanopore sequencing represents a paradigm shift in DNA sequencing, and today it is the only sequencing technology that measures an actual single molecule of DNA, rather than incorporation events into a template strand. In nanopore sequencing, a protein nanopore is attached to a membrane and changes in electronic signal are measured as single molecules of DNA pass through the pore. Oxford Nanopore Technologies (ONT) are a British company who are the first to bring to market a commercial nanopore sequencer. The MinION is the world's first mobile DNA sequencing device, measuring 4" in length and powered by the USB port of a laptop. The MinION is a revolutionary device, and requires a new suite of bioinformatics tools to help work with the data. The MinION presents several technical challenges. Firstly, all sequence files are written to a single directory, regardless of the run or date. All metadata about the run is embedded within the read files themselves, which are in HDF5 format, a hierarchical binary format. The MinION has 512 channels, each designed to hold a single nanopore. Channels write data asynchronously, which means that, unlike other technologies, data can be analysed as soon as it is produced. We have written poRe, one of the first tools that allows users to organise, analyse, extract and visualise MinION data. In this application we intend to further develop poRe, to develop tools for real-time analysis, parallelisation of the code, development of data standards, implementation of a graphical user interface and integration of alignment tools. The latter will be used specifically in the context of veterinary pathogen detection from clinical samples.

Summary

The context of the research: Nanopore sequencing represents a paradigm shift in DNA sequencing, and today it is the only sequencing technology that measures an actual single molecule of DNA, rather than incorporation events into a template strand. In nanopore sequencing, a protein nanopore is attached to a membrane and changes in electronic signal are measured as single molecules of DNA pass through the pore. Oxford Nanopore Technologies (ONT) are a British company who are the first to bring to market a commercial nanopore sequencer. The MinION is the world's first mobile DNA sequencing device, measuring 4" in length and powered by the USB port of a laptop. The MinION is a revolutionary device, and requires a new suite of bioinformatics tools to help work with the data. Aims and objectives: we are one of the first groups in the world to develop and publish a software tool for MinION data. poRe is a package for R that enables users to organise, visualise and analyses MinION nanopore sequencing data. We aim to develop the software further to provide real-time analysis, parallelisation of the code, development of data standards, implementation of a graphical user interface and integration of alignment tools. The latter will be used specifically in the context of veterinary pathogen detection from clinical samples. Potential applications and benefits: we have included letters of support from our users in both UK and international institutes. We believe the future of the MinION is mobile DNA sequencing and thus we have developed poRe to work on the Windows laptop attached to the device, and be easy to install and use. Thus poRe will help enable true mobile sequencing, allowing users to carry out real time sequencing in the field or by the bedside.

Impact Summary

This project will develop unique new features for our software poRe, which is in use in labs throughout the world. Our software allows researchers, both biologists and bioinformaticians, to organise, visualise and analyse MinION nanopore sequencing data. The MinION is a revolutionary device and represents the World's first mobile DNA sequencer. As with any new sequencing technology, the MinION requires new software tools that allow users to interact with the data. poRe is one such software tool. As our letters of support suggest, developing poRe will benefit a huge range of researchers, from graduate students to established professors. A key feature of the software is that it is easy to install and easy to use, therefore our software appeals to biologists who would not normally be able to work with MinION due to the complex data formats produced. The future of the MinION is mobile DNA sequencing, and we anticipate it will be used in the field and by the bedside (i.e. outside of a laboratory) for real-time sequencing. Therefore we have developed poRe to work on a Windows laptop attached to the device, without the need to access remote servers. Obvious applications include vets carrying our real time sequencing in barns and fields for real-time detection if pathogen DNA, and nurses and doctors doing the same by the bedside. Having said that, poRe is also useful in the traditional sense, and is being used by many labs. The beneficiaries of this work will include academic scientists, biotechnology companies, health companies and the health services, vet schools and veterinary practices, the pharmaceutical industry, national governments and the general public.

Committee	Research Committee A (Animal disease, health and welfare)
Research Topics	Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	Tools and Resources Development Fund (TRDF) [2006-2015]
Funding Scheme	X – not Funded via a specific Funding Scheme

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