Episode 86: What's next for nextstrain?
📅7 July 2022
⏱️00:22:55
🎙️Microbial Bioinformatics
👥Guests
University of Bern, Swiss Institute of Bioinformatics
Leo Martins
Head of Phylogenomics, Quadram Institute Bioscience
The microbinfie podcast explores Nextstrain, an innovative bioinformatics platform for tracking and visualizing pathogen evolution, featuring insights from key developers about its technological approach and future potential.
Key Points
1. Nextstrain Platform Overview
- Combination of website (nextstrain.org) and software package
- Uses phylogenetic analysis to track pathogen genome evolution
- Originated in 2014-2015, initially focused on influenza tracking
2. Technical Architecture
- Consists of two primary components: Augur (analysis pipeline) and Auspice (visualization)
- Primarily implemented in Python, with React and JavaScript for web visualization
- Leverages existing computational tools like FastTree and IQtree
3. Collaborative Development Model
- Distributed global team of approximately 10-12 core contributors
- Relies on asynchronous communication via Slack and GitHub
- Extends beyond viruses to include bacterial genome tracking
Take-Home Messages
- Nextstrain provides an accessible platform for tracking pathogen evolution
- Collaborative, open-source approach enables continuous platform improvement
- Visualization and real-time analysis are key strengths of the platform