QCIF partnership delivers game-changing biosecurity tool for Australia's agricultural protection

Every day, scientists at the Department of Agriculture, Fisheries and Forestry (DAFF) analyse samples to identify unknown organisms that could compromise Australia’s biosecurity. These types of analyses are often time-consuming and labour-intensive.

To improve efficiency, the QCIF’s Data and Software Solutions team (DASS) and the QCIF Bioinformatics team– led by Dr Cameron Hyde - worked closely with DAFF experts to document existing procedures and turn them into a reproducible, scalable workflow using Nextflow, a powerful workflow engine that helps streamline complex data analysis.

The result of this collaboration is Taxodactyl, a new bioinformatics workflow that could transform how Australia protects its borders from biological threats.

This milestone is part of the project DNA to Decisions: Concise communication of genomics data for easier decision making”, a collaborative effort between the Department of Agriculture, Fisheries and Forestry (DAFF), Queensland University of Technology (QUT) and Australian BioCommons aimed at transforming biosecurity diagnostics by making standardised bioinformatics workflows and interactive reports accessible to all DAFF biosecurity sites.

Taxodactyl: DAFF’s newest biosecurity upgrade

Developed in collaboration with the Department of Agriculture, Fisheries and Forestry (DAFF) and co-funded by Australian BioCommons, Taxodactyl aims to help DAFF analysts conduct species-level analysis with greater speed, accuracy, and efficiency.

It generates intuitive, visual reports that clearly communicate analytical findings, while providing essential context and transparency for decision-makers.

Bradley Pease, Principal Molecular Biologist at DAFF, says the collaboration has delivered a practical solution to a long-standing challenge in their diagnostics workflow.

“Making sound regulatory decisions that affect global trade is too important to rely on black-box bioinformatics. QCIF worked closely with us to understand the regulatory environment and developed a tool that supports human expertise rather than replacing it. By integrating search results from multiple global databases into a single, interactive report, the tool delivers a significant gain in both productivity and confidence in our decision-making.

The tool is open-source and freely available for use under an MIT license, allowing for adoption across research and biosecurity communities, even internationally.

Strengthening biosecurity through collaboration

The development of Taxodactyl highlights what’s possible when research infrastructure, government, and national platforms work together to tackle shared challenges.

Dr Magda Antczak, bioinformatician at QCIF, will present the project’s outcomes at the upcoming BioCommons Workflows Community Meeting on 2 September 2025, providing an opportunity for community members in the research and government sectors to explore the workflow and consider its application in their own environments.

🔗 Explore the open-source workflow: https://workflowhub.eu/workflows/1782

 📊 View an example workflow report: https://qcif.github.io/taxodactyl/example_report.html 

For more information about the project and to learn more, contact the DASS team.