Interactive real-time metagenomics algorithms for Nanopore sequencing (LEGGETT_E17DTP1)
Lead Research Organisation:
University of East Anglia
Abstract
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Organisations
People |
ORCID iD |
Publications
Cossu G
(2020)
Hemorrhagic direct traumatic carotid-cavernous fistula during endoscopic transsphenoidal surgery: intraoperative management and endovascular treatment.
in Neurosurgical focus: Video
Peel N
(2019)
Semi-quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)
in Methods in Ecology and Evolution
| 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 |