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

Lead Research Organisation: University of East Anglia
Department Name: Graduate Office

Abstract

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.

Publications

10 25 50

Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011216/1 01/10/2015 30/09/2023
1937486 Studentship BB/M011216/1 01/10/2017 30/09/2021 Ned Peel