TYPE OF SUPPORT
Background
Australia is renowned for its strict biosecurity regulations, which safeguard the country’s agriculture and protect native ecosystems from invasive pests and species.
When unknown bugs or microbes are discovered on imported materials, identifying them, and determining whether they pose a risk, becomes critical. Thanks to modern technology, it’s now possible to sequence the DNA of these unknown samples and use computational analysis to confirm their identity.
However, at the federal Department of Agriculture, Fisheries and Forestry (DAFF), these analyses must meet extremely rigorous standards to ensure absolute confidence in the results.
Conventionally, this process can take a DAFF analyst many hours - or even days - of manually-driven computer analyses. With up to 100 samples arriving at each facility each day, the workload quickly becomes immense.
QCIF Role
DAFF engaged QCIF to develop automated workflows that could streamline the analysis process while maintaining the robustness and reliability essential to their operations. The project kicked off in July 2024 with a detailed design phase, during which QCIF’s team worked closely with DAFF analysts to gather analysis requirements and create a series of detailed logic diagrams to map out the analytical details.
Using Nextflow and Python these workflows were built to closely mirror the manual analysis currently performed at DAFF. The workflow generates a client-ready report featuring interactive charts, maps, and tables, making the results clear and accessible for end users.
Outcome & Impact
QCIF has deployed a pilot service on the ARDC Nectar platform and Microsoft Azure cloud compute. This allows DAFF staff to access and run these workflows through a simple web interface, ensuring a consistent, streamlined user experience.
A key outcome of this project is Taxodactyl, a modular, reproducible Nextflow workflow for the conservative taxonomy assignment of DNA sequences, designed to deliver high-confidence, auditable results for biosecurity applications.
Taxodactyl is transforming how biosecurity agencies identify unknown organisms at Australia's borders, replacing manual, time-intensive DNA analysis with a fast, standardised and reproducible workflow. By enabling more consistent, scalable and reliable decision-making, it helps authorities respond to potential biosecurity threats with greater speed and confidence.
Developed as an open-source solution, Taxodactyl has the potential for delivering benefits far beyond a single use case. The workflow could support advances across biosecurity, agriculture and environmental research, creating new opportunities for collaboration, innovation and knowledge sharing across sectors.
In recognition of this achievement, the project team received the 2026 Queensland iAward in the Not-for-Profit and Community category, which celebrates technology innovations that deliver meaningful social impact and make a tangible difference to communities, industries and society.
This project has been a fantastic challenge for the team, as it combines bioinformatics with software engineering to meet tough stakeholder requirements. This is exactly the kind of work that our team thrives on.
Dr Cameron Hyde, Senior Software Developer, QCIF
Collaborating Organisations
Australian BioCommons; Bradley Pease (DAFF) – principal investigator; Roberto Barrero Gumiel (QUT lead) – subcontractor; Marie-Emilie Gauthier (QUT bioinformatician) - subcontractor
