What to know
The Centre for Genomic Pathogen Surveillance (CGPS) at the University of Oxford developed software tools to gather, integrate, and visualize genomic sequence data. These applications incorporated many different types of data. Awarded in 2021, this project built customized data roadmaps at state-level laboratories acting as pilot sites. Researchers, in collaboration with CDC, analyzed the bioinformatics capacity, data systems, and reporting processes within strategically identified sites. Protocol and training materials created for the developed toolchain provided a wider range of genomic surveillance support.
New and improved sequencing software tools
The CGPS continued to develop a suite of tools for genomic epidemiology analysis and visualization and has partnered with five state public health departments (Idaho, Utah, Wyoming, Washington, and New Mexico) to pilot these tools for SARS-CoV-2.
- Microreact is an open source, web-based tool for interactive visualization and data exploration. It enables the rapid generation and linkage of trees, maps, networks, charts, and timelines, empowering epidemiologists and key decision-makers to react rapidly and with greater accuracy.
- Data-flo is an open source, web-based tool for modular, easily customizable integration and manipulation of data via a simple drag-and-drop interface. Data-flo easily combines epidemiological data, genomic data, laboratory data, and various metadata from disparate sources (i.e., different data systems) and formats.