Nextstrain is an open-source platform that exploits genome data to facilitate the investigation of pathogen spread and evolution in real time. Nextstrain allows health professionals, researchers, and the public to see the history of an epidemic by providing updated analyses and visualizations of publicly available and curated pathogen genomic data in a single website. The project also provides open-source software toolkits to allow interested parties to analyze and visualize their own pathogen genomic data. The toolkits include bioinformatic pipelines for genome-wide phylogenetic analysis and interactive visualizations of genomic data over space and time.
Example of SARS-CoV-2 data visualization provided by Nextstrain. By visiting the Nextstrain website, you can easily see the latest analyses regarding SARS-CoV-2 phylogeny over time, how lineages are distributed geographically, and the diversity observed across the genome (variability per genome position).
CZ GEN EPI and Nextstrain
CZ GEN EPI provides a no-code web interface that allows users to easily build Nextstrain trees using their own SARS-CoV-2 data. That’s right! CZ GEN EPI users get their own up-to-date SARS-CoV-2 trees without any coding or having to search for the latest publicly available sequences or having to download software. CZ GEN EPI handles data management and uses Nextstrain toolkits to build trees. Trees are built automatically on a daily basis or on-demand (see guides regarding tree types, how to build them, and tree viewing). Users can access and manage the resulting tree builds from their CZ GEN EPI Phylogenetic Tree page to evaluate outbreak dynamics in their jurisdictions. The diagram below provides an overview of the workflow used to build Nextstrain trees from CZ GEN EPI.
Workflow for building Nextstrain phylogenetic trees from CZ GEN EPI.