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

Oxford Nanopore Technologies（ONT）MinION是一款令人兴奋的新型DNA测序仪，于2014年以预发布形式上市。它提供多个读段，由于其紧凑的尺寸、低成本和流操作模式，能够在生成数据时进行分析，因此引起了人们的兴趣。MinION代表了第一个真正的便携式测序平台，能够在现场与样本收集一起部署，使其非常适合宏基因组和环境测序应用。尽管MinION令人兴奋，但分析工具和管道目前落后，难以实现该设备的潜力;通常用户离线分析数据，而不是利用平台的实时功能，并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颖的技术来利用MinION的实时性，在主管之前工作的基础上再接再厉。这包括（1）开发用于宏基因组序列数据的流式分类和分析的方法（2）利用ONT的Read Until编程接口通过分析原始信号数据从混合样品中选择性地测序（3）用于与数据交互和可视化数据的方法。

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.