Episode 131: Bioinformatics Evolution: Torsten Seemann on Snippy, Open-Source Support, and Global Genomics
👥Guest
In this episode of the Micro Binfie Podcast, host Andrew Page catches up with Torsten Seemann at the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. They discuss the rapid evolution of bioinformatics, the challenges faced by labs worldwide, and the explosion of tools post-COVID. Torsten shares insights into his work at Melbourne’s Microbiological Diagnostic Unit (MDU), the development of platforms like OzTracker for bacterial genomics, and how his lab plays a national and international role in data sharing.
The conversation dives into the future of the widely-used variant calling tool Snippy, as Torsten reveals exciting updates funded by the Chan Zuckerberg Initiative, including nanopore read support and the ability to process pre-assembled genomes. They also explore the importance of maintaining open-source bioinformatics tools to prevent them from becoming obsolete. Tune in for an in-depth discussion on the state of genomics, software development, and the challenges and rewards of open-source collaboration.
Key Points
1. Bioinformatics Landscape
- Significant growth in genomics tools and capabilities post-pandemic
- Challenges faced by international partners in implementing bioinformatics solutions
- Increasing complexity and diversity of available tools
2. OzTracker and National Collaboration
- Development of a surveillance platform for sharing genomic data across Australian state labs
- Expanding national and international data sharing capabilities
- Integration with global platforms like NCBI and WHO
3. Snippy Tool Development
- Secured Chan Zuckerberg Initiative grant for software maintenance
- Planning Snippy Next Generation (Snippy NG) with new features
- Upcoming support for nanopore reads and pre-assembled genomes
Take-Home Messages
- Maintaining open-source bioinformatics tools is crucial for scientific progress
- Collaborative efforts are key to advancing genomic research globally
- Continuous adaptation and funding are essential for software sustainability