Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification
FP Breitwieser, SL Salzberg - Bioinformatics, 2020 - academic.oup.com
Bioinformatics, 2020•academic.oup.com
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 …
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 …
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.
Oxford University Press