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

点击翻译按钮获取中文摘要

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.