(Maximum 1.5 pages)
- How will this project position PFR for future funding opportunities?
- What will success of this 1-2 year project look like in science terms e.g. Capability / platform development, know-how, IP, papers, and/or technology produced by the end of the funding term, collaborations developed or strengthened. Bullet point format preferred.
- Note the timeline and key milestones (e.g. decision points, outputs or key steps) for achieving the stated outcome and deliverables for this 1-2 year project.
This project will position PFR for future funding applications by strenghtening our capabilities in variant calling applied to genome-informed breeding. Such capabilities will be crucial for future funding for pipfruit, kiwifruit, arable crops and finfish breeding.
This project aims at supporting automation initiatives within PFR as well as on a global stage. It is impossible to generate a comprehensive framework in the given time frame. Further work will be needed. Within this project success in two years will look as follows:
- A baseline for comparing variant calling pipelines will have been developed
- The framework will have been developed and published in the Catalyst cloud
- We will have published reseach papers establishing an interpretive context for variant calling
- A new way to deliver high value markers and other breeding technology will have been developed.
- Database of SNPs with associated certainty values
Capability in rigorously calling variants and assessing their value in species of interest.
Knowledge of biological and technical effects on each of the pipelines' ability to correctly call variants (ROC).
During the programme we will:
- Produce an open source trusted reproducible research framework for calling variants from GBS and resequencing data sets.
- Automation of variant calling pipelines with trusted results
- Plug and play usability for end users
- A usable framework with a clear path for continuous improvement.
- Establishing the scientific value of developing an interpretive context.
| Milestone | Metric of success | Year |
|---|---|---|
| Example data acquired | availability of required example data | 1 |
| Test data simulated | workflow for generating test data | 1 |
| Cloud platform established | Availability of a cloud solution for data analysis | 1 |
| Baseline developed | comparative metrics for different pipelines available | 2 |
| Rack framework developed | Pipelines and data available in a rack | 2 |
| 5 pipelines tested against baseline | Differences between pipelines established | 2 |
| Matrix of datasets and tools | Availability of online resource with decision support | 2 |