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28 Jun 2024

Associate Professor Seemann awarded Essential Open Source Software for Science Grant for global microbial genomics research

The Chan Zuckerberg Initiative (CZI) has awarded an Essential Open Source Software for Science grant to the University of Melbourne’s Associate Professor Torsten Seemann, Lead Bioinformatician in The Centre for Pathogen Genomics at the Doherty Institute.

The USD$260,000 grant will support two years of development for Snippy, an open-source software tool for rapidly identifying genetic differences between bacterial genome sequences. This work will allow Snippy to support the latest genome sequencing technologies and viral and fungal pathogens.

Original developer of the software, Associate Professor Seemann said an upgrade is urgently needed to ensure Snippy continues to serve the microbial genomics research community for the next decade.

“Thanks to the CZI’s support over the next two years, we will modernise Snippy’s implementation to meet current best practice in software engineering, support new types of sequencing data from a wider range of pathogens, improve the testing framework, and future-proof the software by making it modular and easy to extend over time,” said Associate Professor Seeman.

This work will be undertaken with postdoctoral researcher University of Melbourne Dr Wytamma Wirth, a skilled bioinformatician currently working alongside Associate Professor Seemann.

For the past 10 years, Snippy has been widely recognised as a leading tool for detecting genomic variants in bacteria, assisting over 2,000 research projects in the study of bacteria, their evolution and how they cause diseases.

Snippy facilitates variant calling, a process crucial for numerous scientific studies, including investigating anti-microbial resistance, constructing phylogenetic trees to track outbreaks, validating laboratory mutants and conducting genome-wide association studies (GWAS) to uncover links between a pathogen’s genome and its capacity to causes disease.

Created in Melbourne, Australia, Snippy is deployed in public health and clinical microbiology settings globally. In particular, it is widely used in low-resource settings in Asia-Pacific and Africa due to its accessibility and user-friendly operation. Users enjoy its clear documentation, minimal operating requirements and compatibility with lower-spec computers.

University of Melbourne’s Professor Paul Gorry, Deputy Director at the Doherty Institute, congratulated Associate Professor Seeman, stressing the crucial role of software in scientific research.

“Software tools are indispensable in modern scientific research as they enable more complex analyses and contribute to significant advancements in various fields. We expect that Snippy will continue to be a reliable asset in global microbial genomics research,” said Professor Gorry.

The Chan Zuckerberg Initiative was founded in 2015 to help solve some of society’s toughest challenges — from eradicating disease and improving education, to addressing the needs of our communities. Their Essential Open Source Software for Science program supports software maintenance, growth, development and community engagement for critical open-source tools. Find out more here.