PT  - JOURNAL ARTICLE
AU  - Florian P. Breitwieser
AU  - Steven L. Salzberg
TI  - Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification
AID  - 10.1101/084715
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 084715
4099  - http://biorxiv.org/content/early/2016/10/31/084715.short
4100  - http://biorxiv.org/content/early/2016/10/31/084715.full
AB  - Summary 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.Availability and implementation Pavian 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.Contact fbreitw1{at}jhu.eduSupplementary information Supplementary data is available at Bioinformatics online.