New software for nanopore based diagnostics and surveillance

牛津纳米孔技术公司的MinION是一款由英国技术开发的新型DNA测序仪，它只有几英寸长，可以插入笔记本电脑的USB接口。其低成本和便携性使其对“现场”和临床测序应用极具吸引力。这类样本通常是宏基因组（许多不同生物的混合样本），研究人员想要回答的关键问题通常是：1)样本中有哪些物种？每种有多少？3)有哪些抗生素耐药菌？与之前的测序技术不同，MinION能够实时工作，这意味着数据可以在生成时逐步分析。在临床环境中，这可能意味着比其他方式更快地获得测试结果。然而，缺乏能够执行实时分析的软件，许多用户未能利用该技术的这一独特功能。该项目的目的是开发一种软件工具，可以以易于安装和使用的方式提供临床和环境样品的实时分析，但它可以根据个人应用的具体需求定制分析。我们也非常渴望利用MinION可以比旧技术测序更长的DNA片段的事实，以便更准确地识别具有抗生素耐药性的细菌。最终，这将导致改进与细菌有关的疾病的治疗方案。

The Oxford Nanopore Technologies MinION is a new DNA sequencer developed in the UK from UK technology, it is only a few inches long and plugs into the USB port of a laptop. Its low cost and portability make it extremely attractive for "in field" and clinical sequencing applications. These kinds of samples are typically metagenomic (mixed samples of many different organisms) and often the key questions researchers want to answer are: 1) what species are in the sample? 2) how much of each is there? 3) What kinds of antibiotic resistance bacteria are there?Unlike previous sequencing technologies, the MinION is capable of working in real-time, which means that data can be analysed progressively as it is generated. In a clinical setting, this could mean getting test results back far quicker than would otherwise be possible. However there is a lack of software capable of performing real-time analysis and many users fail to take advantage of this unique feature of the technology. The aim of this project is to develop a software tool that can provide real-time analysis of clinical and environmental samples in an easy-to-install and easy-to-use way, but which enables tailoring of the analysis to the specific needs of individual applications. We are also very keen to take advantage of the fact that the MinION can sequence much longer stretches of DNA than older technologies in order to more accurately identify the bacteria which harbour antibiotic resistance. Ultimately, this will lead to improved treatment regimes for illnesses linked to bacteria.