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

Abstract 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...

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Bibliographic Details
Published inBioinformatics Vol. 36; no. 4; pp. 1303 - 1304
Main Authors Breitwieser, Florian P, Salzberg, Steven L
Format Journal Article
LanguageEnglish
Published England Oxford University Press 15.02.2020
Subjects
Applications Notes
Data Interpretation, Statistical
Metagenomics
Microbiota
Software
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Summary:Abstract 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.
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ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btz715