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

poRe：纳米孔测序数据的可视化和分析，用于快速移动病原体检测

• 批准号: BB/M020037/1
• 负责人: Michael Watson
• 金额: $ 18.94万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM020037%2F1
• 关键词: poRe; visualization; analysis; nanopore; sequencing

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.

研究背景：纳米孔测序代表了DNA测序的范式转变，今天它是唯一测量实际单个DNA分子的测序技术，而不是将事件掺入模板链中。在纳米孔测序中，蛋白质纳米孔附着在膜上，并且当DNA的单个分子通过孔时测量电子信号的变化。Oxford Nanopore Technologies（ONT）是一家英国公司，是第一家将商业纳米孔测序仪推向市场的公司。MinION是世界上第一台移动的DNA测序设备，长度为4”，由笔记本电脑的USB端口供电。MinION是一种革命性的设备，需要一套新的生物信息学工具来帮助处理数据。目的和目标：我们是世界上最早开发和发布MinION数据软件工具的团队之一。poRe是R的一个软件包，使用户能够组织，可视化和分析MinION纳米孔测序数据。我们的目标是进一步开发软件，以提供实时分析，代码的并行化，数据标准的开发，图形用户界面的实施和对齐工具的集成。后者将专门用于从临床样品中检测兽医病原体。潜在的应用和好处：我们已经包括了来自英国和国际机构的用户的支持信。我们相信MinION的未来是移动的DNA测序，因此我们开发了poRe，可以在连接到设备的Windows笔记本电脑上工作，并且易于安装和使用。因此，poRe将有助于实现真正的移动的测序，允许用户在现场或床边进行真实的时间测序。

项目成果

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.

• DOI: 10.1093/gigascience/gix007
• 发表时间: 2017-03-01
• 期刊: GigaScience
• 影响因子: 9.2
• 作者: Brown BL;Watson M;Minot SS;Rivera MC;Franklin RB
• 通讯作者: Franklin RB

poRe: an R package for the visualization and analysis of nanopore sequencing data.

• DOI: 10.1093/bioinformatics/btu590
• 发表时间: 2015-01-01
• 期刊: Bioinformatics (Oxford, England)
• 作者: Watson M;Thomson M;Risse J;Talbot R;Santoyo-Lopez J;Gharbi K;Blaxter M
• 通讯作者: Blaxter M

A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data.

• DOI: 10.1186/s13742-015-0101-6
• 发表时间: 2015
• 期刊: GigaScience
• 影响因子: 9.2
• 作者: Risse J;Thomson M;Patrick S;Blakely G;Koutsovoulos G;Blaxter M;Watson M
• 通讯作者: Watson M

poRe GUIs for parallel and real-time processing of MinION sequence data

用于并行实时处理 MinION 序列数据的 poRe GUI

• DOI: 10.1101/094979
• 发表时间: 2016
• 作者: Stewart R