At NSW DPIRD, I’m developing software to help researchers design and assess DNA-based tests for plant pathogens. The pipeline brings together genome sequence data, diagnostic test design and quality checks, reducing the amount of manual analysis needed to identify reliable tests.
- Collect. Automates the download and preparation of all public DNA sequences for any organism of interest and its off-targets.
- Find suitable DNA targets. Compares pathogen genomes with plant hosts and closely related organisms to identify DNA regions that can help distinguish the pathogen from other species.
- Design diagnostic tests. Generates every feasible assay within those regions, maximising coverage of known variants of the pathogen. It supports PCR, qPCR, LAMP, RPA and CRISPR-based assays, as well as multiplex assays and degenerate primers that accommodate natural sequence variation.
- Quality control and coverage. Filters candidates through quality control for dimers, hairpins, homopolymers, GC%, and Tm, then calculates variant coverage for surviving primers.
- Compare and report candidates. Ranks the strongest designs and reports which proportion of the known pathogen variants each is expected to detect, helping researchers decide which tests to investigate further.
The software can also assess primers that researchers have already designed, estimate which pathogen variants they are likely to detect, and suggest improved alternatives. A graphical interface is intended to make the pipeline usable by researchers without specialist bioinformatics skills, while adjustable settings allow experienced users to tailor the analysis.
- Status
- In development
- Built by
- NSW DPIRD, in collaboration with Deakin University
- Funding
- Australian Government Department of Agriculture, Fisheries and Forestry (DAFF)
- Validation
- Deakin University is testing the pipeline on three different pathogen systems