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MicrobeTrace is an intuitive, powerful, free web-browser based application that uses a combination of genomic and/or epidemiological data to display customizable networks and other visuals.
The visualization can be customized using supplemental data sources like demographic data, geospatial data and mathematical inferences like the most probable transmission pathways. MicrobeTrace is a highly responsive, visual sequence analytics tool which overlay genomic and epi data using simple point and click interfaces , reducing the gap between data production and analytics and help you to discover, understand, and display relationships between patients, pathogen sequences or places (nodes). MicrobeTrace can be deployed on laptops to locations without any Internet access, thereby reducing both the startup cost and analysis time and effort. Click on the video link below to get a 2 minute glimpse of what the tool can do!
Read the flyer for a quick glimpse
Original publication describing the tool MicrobeTrace: Retooling molecular epidemiology for rapid public health response
NOTE: When you click on the link above and accept the EULA, MicrobeTrace will be automatically installed on your PC.
Read through the rest of the page for training resources before you try the tool.
If you'd rather just reach us to ask questions or would like a live demonstration of the tool, email us at : microbetrace@cdc.gov
Download and read the user manuals below- now available in multiple languages!!
ENGLISH (https://github.com/CDCgov/MicrobeTrace/files/9577093/MicrobeTrace_User_Manual_v0.6.2_Oct_2021.pdf)
SPANISH (https://github.com/CDCgov/MicrobeTrace/raw/master/docs/MicrobeTrace_manual_May_2021_Espanol_508.docx)
MANDARIN (https://github.com/CDCgov/MicrobeTrace/raw/master/docs/21_325559-A_MicrobeTrace_final_Chinese.pdf)
If you prefer watching a demo, click below for the training webinar
https://www.youtube.com/watch?v=5E-_Kb7yvHU)
- Watch the quick user guide
- Watch MicrobeTrace - Overview
- Watch MicrobeTrace - Design and development
- System Requirements
- Download Sample Data NOTE: Please select TN93 as the distance metric when you use this downloaded sample data
- Watch Using MicrobeTrace - Loading files
- Watch Using MicrobeTrace - Loading and aligning sequence data
- Watch Using MicrobeTrace - Overlaying genetic distance network with edge list data
Types of Files:
Special Files:
Simulated Data:
| View | Docs | Demo |
|---|---|---|
| 2D Network | Read 🗎 | Watch |
| Table | Read 🗎 | Watch |
| Aggregation | Read 🗎 | Watch |
| Bubbles | Read 🗎 | Watch |
| Flow Diagram | Read 🗎 | Watch |
| Waterfall | Read 🗎 | Watch |
| Map | Read 🗎 | Watch |
| Gantt | Read 🗎 | Watch |
| Timeline | Read 🗎 | |
| Heatmap | Read 🗎 | Watch |
| Phylogenetic Tree | Read 🗎 | Watch |
| Sequences | Read 🗎 | Watch |
As of February 2026, MicrobeTrace has received more than 18,000 visitors, including over 13,000 users, and has accumulated more than 30,000 total site visits. The bar chart shows annual visitor counts from 2018 through 2026, highlighting significant growth during the COVID‑19 pandemic in 2021 and 2022. Click the image to open the published dashboard in Tableau Public and explore total counts of visitors and users.