Computer Science and Engineering
Nanopore sequencing, a vital genomic technology, utilises Oxford Nanopore Technologies (ONT) devices to analyse both short and long-native DNA and RNA molecules, holding diverse potential in life sciences. These devices measure ionic current changes as DNA/RNA passes through a nanoscale protein pore, recording 'squiggle' data. Data simulation, crucial for scientists and developers, aids in testing, debugging, and validating new analysis methods without real-world variables. It's used for hypothesis development, experimental design, and benchmarking. The Squigulator was introduced as a tool to generate nanopore current signal data, closely resembling real data from a nanopore device, with 99% similarity to the R9.4.1 chemistry. The upcoming R10.4.1 pore chemistry differs, achieving only 90% similarity. The project's aim is to identify modelling techniques to enhance simulated data for R10.4.1, aligning it more closely with real data.
School
Research Areas
Bioinformatics | Genomics | Data analysis | Computational biology
- Research Environment
- Expected Outcomes
- Supervisory Team
- Reference Material/Links
You will be working with me (Hasindu Gamaarachchi - lecturer in bioinformatics), PhD students and undergraduate honours students in our group. You will also collaborate with researchers at the nanopore sequencing facility of Garvan Institute of Medical Research for learning about up-to-date information about cutting-edge nanopore sequencing. Bioinformatics students who are ready to take on this challenging project are welcome to apply.
A method/model to accurately simulate raw nanopore signal data for the R10.4.1 pore chemistry than what is possible currently through the state-of-the-art.
