At NSW DPIRD I’m building a software pipeline that automates the design and checking of molecular diagnostic tests for pathogens. It handles everything from acquiring sequence data to finding diagnostically relevant regions to designing assays (PCR, qPCR, LAMP, RPA and CRISPR) and performing comprehensive quality control.
- Collect. Downloads and prepares genome sequences for any organism of interest.
- Find targets. Locates the DNA regions that tell the target apart from plant hosts and closely related species.
- Design. 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 designs and degenerate primers that accommodate natural sequence variation.
- Quality control. Screens each design for problems that cause assays to fail, including primers that bind themselves or each other (dimers and hairpins), runs of repeated bases, and poorly matched melting temperatures.
- Report. Ranks the best candidates and reports how many known variants of the species each one detects.
A second mode evaluates primers you have already designed. It reports how well they perform and how many variants they capture, and can suggest improved primers that target the same region.
A graphical interface makes the software accessible to non-specialists, while adjustable thresholds and settings give experienced users full control.
- 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