The Chan Zuckerberg Initiative (CZI) has awarded an Essential Open Source Software for Science grant to Associate Professor Torsten Seemann, Lead Bioinformatician at the Centre for Pathogen Genomics, Doherty Institute, University of Melbourne. The USD$260,000 grant will fund two years of development for Snippy, an open-source tool designed to rapidly identify genetic differences between bacterial genomes.

The grant will enable Snippy to support the latest genome sequencing technologies, extending its reach to viral and fungal pathogens. According to Associate Professor Seemann, Snippy urgently requires this upgrade to continue serving the global microbial genomics community.

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

The development work will be led by Associate Professor Seemann, alongside postdoctoral researcher Dr. Wytamma Wirth, a bioinformatician at the University of Melbourne.

For the past decade, Snippy has been a key tool for microbial genomics, assisting over 2,000 research projects in investigating bacterial evolution, disease mechanisms, and antimicrobial resistance. Snippy’s functionality in variant calling is essential for research into pathogen evolution, outbreak tracking through phylogenetic trees, genome-wide association studies (GWAS), and the study of laboratory mutants.

Developed in Melbourne, Australia, Snippy is used in public health and clinical microbiology settings worldwide, particularly in low-resource regions like Asia-Pacific and Africa. Its popularity stems from its clear documentation, minimal system requirements, and ease of use, even on lower-spec computers.

Professor Paul Gorry, Deputy Director at the Doherty Institute, congratulated Associate Professor Seemann and emphasised the importance of software tools in modern scientific research:

“Software tools are indispensable in modern research, enabling complex analyses that drive significant advancements. We anticipate that Snippy will continue to be a vital resource in global microbial genomics research.”

Founded in 2015, the Chan Zuckerberg Initiative aims to tackle society’s biggest challenges, from eradicating disease to improving education. The Essential Open Source Software for Science program focuses on maintaining, developing, and engaging the community around critical open-source tools. You can learn more about their mission here.