Interactive real-time metagenomics algorithms for Nanopore sequencing (LEGGETT_E17DTP1)

牛津纳米孔技术(ONT)是一款令人兴奋的新DNA测序仪，于2014年发布前发布。它提供几千个基数的读取，由于其紧凑的大小、低成本和支持在生成数据时分析数据的流操作模式而吸引了人们的兴趣。Minion代表了第一个真正的便携式测序平台，能够与样本采集一起部署在现场，使其非常适合于元基因组和环境测序应用。尽管与Minion相关的激动人心，但分析工具和管道目前落后，使得该设备的潜力很难实现；通常用户离线分析数据，而不是利用平台的实时功能，而且通常涉及许多手动步骤。在这个项目中，我们的目标是研究一些新的技术，以利用Minion的实时特性，建立在监督者之前的工作基础上。这包括(1)开发元基因组序列数据的流分类和分析方法(2)利用ONT的Read Under编程接口通过分析原始信号数据从混合样本中选择性地进行序列测定(3)与数据交互和可视化的方法。

The Oxford Nanopore Technologies (ONT) MinION is an exciting new DNA sequencer that arrived in prerelease form in 2014. Offering multi-kilobase reads, it attracted interest due to its compact size, low cost, and a streamed mode of operation enabling analysis of data as it is generated. The MinION represents the first truly portable sequencing platform capable of being deployed in the field alongside sample collection, making it ideally suited to metagenomic and environmental sequencing applications. Despite the excitement associated with the MinION, analysis tools and pipelines currently lag behind, making it difficult to realise the potential of the device; typically users analyse data offline, rather than exploiting the real-time functionality of the platform, and there are often many manual steps involved.In this project, we aim to research a number of novel techniques for exploiting the real-time nature of the MinION, building upon previous work of the supervisors. This includes (1) developing approaches for streamed classification and analysis of metagenomic sequence data (2) utilising ONT's Read Until programming interface to selectively sequence from a mixed sample by analysis of raw signal data (3) approaches for interacting with and visualising data.