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. 2020 Feb 15;36(4):1303-1304.
doi: 10.1093/bioinformatics/btz715.

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

Florian P Breitwieser  1 , Steven L Salzberg  2
Affiliations

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

Florian P Breitwieser et al. Bioinformatics. .

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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Figures

Fig. 1.
Fig. 1.
(A) Main interface with sample classification summary shown in a Sankey diagram. The width of the flow corresponds to the number of reads, and hovering over a species node brings up a barchart with the number of reads for the species across the sample set (inset). (B) The sample comparison module provides a tabular overview of the reads, percentages or z-scores over all samples at any taxonomic rank with interactive filtering. (C) The alignment viewer displays the coverage of a particular genome based on BAM alignment files
See this image and copyright information in PMC

References

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    1. Breitwieser F.P. et al. (2018) KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biol., 19, 198. - PMC - PubMed
    1. Breitwieser F.P. et al. (2017) A review of methods and databases for metagenomic classification and assembly. Brief. Bioinform. doi: 10.1093/bib/bbx120. - PMC - PubMed
    1. Kim D. et al. (2016) Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res., 26, 1721–1729. - PMC - PubMed
    1. McMurdie P.J., Holmes S. (2015) Shiny-phyloseq: web application for interactive microbiome analysis with provenance tracking. Bioinformatics, 31, 282–283. - PMC - PubMed

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