Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification

SUMMARY: Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize and transform results from various classifiers-such as Kraken, Centrifuge and MethaPhlAn-using interactive data tables, heatmaps and Sankey flow diagrams. An interactive alignment coverage viewer can help in the validation of matches to a particular genome, which can be crucial when using metagenomics experiments for pathogen detection. AVAILABILITY AND IMPLEMENTATION: Pavian is implemented in the R language as a modular Shiny web app and is freely available under GPL-3 from http://github.com/fbreitwieser/pavian.

• NI
  National Institutes of Health

  Awards: R01-HG006677, HG006677, R35-GM130151
• AR
  Army Research Office

  Awards: W911NF-14-1, W911NF, W911NF-14-1-0490