CCB » Software » Pavian

About Pavian

Pavian is a web application for exploring metagenomics classification results, with a special focus on infectious disease diagnosis. Pinpointing pathogens in metagenomics classification results is often complicated by host and laboratory contaminants as well as many non-pathogenic microbiota. With Pavian, researchers can analyze, display and transform results from the Kraken and Centrifuge classifiers using interactive tables, heatmaps and flow diagrams. Pavian also provides an alignment viewer for validation of matches to a particular genome.

Source code and most up-to-date documentation is available at

Preprint now available at


Installing and running Pavian

In R / RStudio:

## Installs required packages from CRAN and Bioconductor
## The above command no longer works in R Studio (as of 2020). Try this instead:

With Docker:

docker run -p 5000:80 florianbw/pavian

In both cases Pavian will be available at .

Licensing and Contact Information

Pavian is open source, licensed under GPLv3.


Florian Breitwieser ( fbreitw1 jhmi edu )
Steven Salzberg