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

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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
 
Title 3D nanopore model 
Description The model consists of a 3D printed CsgG protein pore, which is the protein used in Oxford Nanopore Technologies' sequencing devices, and a 3D printed single-stranded DNA molecule. 
Type Of Art Artefact (including digital) 
Year Produced 2019 
Impact This 3D model is used at public engagement events, such as the Earlham Institute open day and 2019 Norwich Science Festival, to demonstrate how nanopore-based DNA sequencing works to members of the general public. 
 
Title Reverse Metagenomics (RevMet) 
Description RevMet (Reverse Metagenomics) is a method that allows reliable and semi-quantitative characterisation of the species composition of mixed-species eukaryote samples, such as bee-collected pollen, without requiring assembled reference genomes. Instead, reference species are represented only by 'genome skims': low-cost, low-coverage, short-read datasets. The skims are mapped to long reads sequenced from mixed-species samples, using nanopore sequencing, and the long reads are uniquely assigned to eukaryote species. 
Type Of Material Biological samples 
Year Produced 2019 
Provided To Others? Yes  
Impact The RevMet method is currently being applied by other researchers for the purpose of characterising bee-collected pollen. 
URL https://revmet.readthedocs.io/en/latest/index.html
 
Description Norwich Science Festival 2018 - NedOME 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact We showcased our research on real-time DNA sequencing. Using using the MinION, a portable DNA sequencer developed by Oxford Nanopore Technologies, we sequenced and analysed a human genome (the NedOME) in real-time at the Norwich Science Festival 2018. The demonstration led to very interesting discussions with members of the public.
Year(s) Of Engagement Activity 2018
 
Description Norwich Science Festival 2019 - Bee trail 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact We combined our LEGO DNA sequencer with a trail based activity to communicate our bee-collected pollen sequencing research (https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13265). The trail took members of the public on a clue-hunting tour of discovery, where they had to find bees and the plants that they pollinate. Attached to each bee was a pollen grain sticker with a unique DNA sequence. The sequence could be built out of LEGO and put through our LEGO DNA sequencer to discover what plant each bee had been visiting. At the end of the trail participants received a bag of wildflower seeds and were encouraged to share pictures and videos as they plant these in their gardens or other areas set aside for cultivating wildflower meadows.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/articles/barney-bee-buzzing-norwich-science-festival