Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification
Abstract
SummaryPavian 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.\n\nAvailability and implementationPavian is implemented in the R language and based on the Shiny framework. It can be hosted on Windows, Mac OS X and Linux systems, and used with any contemporary web browser. It is freely available under a GPL-3 license from http://github.com/fbreitwieser/pavian. Furthermore a Docker image is provided at https://hub.docker.com/r/florianbw/pavian.\n\nContactfbreitw1@jhu.edu\n\nSupplementary informationSupplementary data is available at Bioinformatics online.
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Abstract summary
Claude Opus 5.5 · xhigh effort · 2 Nov 2026 · from the abstract
Pavian is an R Shiny web application that visualizes and transforms Kraken and Centrifuge metagenomics classification outputs using interactive tables, heatmaps, flow diagrams, and a genome alignment viewer.
Identifying pathogens in metagenomics classification outputs is frequently confounded by host and laboratory contaminants as well as abundant non-pathogenic microbiota. Pavian provides an interactive web interface to inspect, transform, and validate classification results from Kraken and Centrifuge for infectious disease diagnostics and microbiomics.
Key results
ClaimedPavian enables interactive visual exploration, transformation, and validation of metagenomics classification results from Kraken and Centrifuge.
Implemented in R using the Shiny framework for Windows, Mac OS X, and Linux, the tool provides interactive tables, heatmaps, flow diagrams, and a genome alignment viewer to inspect matches to specific genomes (no quantitative benchmarks are reported in the abstract). · Abstract
Methods, data and reproducibility
Pavian was built as an R web application using the Shiny framework to ingest outputs from the Kraken and Centrifuge metagenomics classifiers. It renders interactive tables, heatmaps, flow diagrams, and a genome alignment viewer accessible via standard web browsers or a Docker container.
- Methods & tools
- Pavian, R, Shiny, Kraken, Centrifuge, Docker
- Software & environment
- Implemented in R with the Shiny framework; runs on Windows, Mac OS X, and Linux; Docker image available at https://hub.docker.com/r/florianbw/pavian.
- Reproducibility gaps
- No specific benchmark datasets, accession numbers, or computational resource requirements are reported in the abstract.
Limitations (2)
- The abstract describes software features only and reports no quantitative evaluation, benchmark datasets, or diagnostic performance metrics. · noted in this summary
- Input support described in the abstract is restricted to outputs from the Kraken and Centrifuge classifiers. · noted in this summary
Who should read:Read this if you use Kraken or Centrifuge for metagenomics classification and want an interactive R Shiny web interface to inspect classification results and genome alignments.
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