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

Florian P. Breitwieser; Steven L. Salzberg

doi:10.1093/bioinformatics/btz715

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

Florian P. Breitwieser, Steven L. Salzberg

School of Medicine

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English (US)
Pages (from-to)	1303-1304
Number of pages	2
Journal	Bioinformatics
Volume	36
Issue number	4
DOIs	https://doi.org/10.1093/bioinformatics/btz715
State	Published - Feb 15 2020

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btz715

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abstract = "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.",

author = "Breitwieser, {Florian P.} and Salzberg, {Steven L.}",

note = "Funding Information: This work was supported in part by grants R35-GM130151 and R01-HG006677 from the National Institutes of Health, and by grant number W911NF-14-1-0490 from the U. S. Army Research Office. Publisher Copyright: {\textcopyright} 2020 Oxford University Press. All rights reserved.",

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N2 - 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.

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

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ASJC Scopus subject areas

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