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.
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.
Organisations
People |
ORCID iD |
| Richard Leggett (Primary Supervisor) | |
| Ned Peel (Student) |
Publications
Peel N
(2019)
Semi-quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)
in Methods in Ecology and Evolution
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011216/1 | 01/10/2015 | 31/03/2024 | |||
| 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 |