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

University of East Anglia - School of Biological Sciences

Start Date:  1st October 2017

No. of positions available: 1

Supervisor: Dr Richard Leggett

Project description: 
The Oxford Nanopore Technologies (ONT) MinION is an exciting new DNA sequences 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.

Person specification:  
The successful candidate will be trained in computer science, software engineering or bioinformatics and will work to develop algorithms to enable the implementation of an interactive real-time analysis package for nanopore-based researchers. This project builds upon the deep technical and biological expertise at the Norwich Research Park, and the new technology has applications in a range of settings, including clinical and environmental genomics – providing a wealth of opportunities for an ambitious candidate.

Funding notes: 
Full Studentships cover a stipend (RCUK rate: £14,296pa – 2016/7), research costs and tuition fees at UK/EU rate, and are available to UK and EU students who meet the UK residency requirements.

Students from EU countries who do not meet the UK residency requirements may be eligible for a fees-only award. Students in receipt of a fees-only award will be eligible for a maintenance stipend awarded by the NRPDTP Bioscience Doctoral Scholarships, which when combined will equal a full studentship. To be eligible students must meet the EU residency requirements.

Details on eligibility for funding on the BBSRC website:

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