Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification
By Florian P. Breitwieser, Steven L. Salzberg. Bioinform., 2019
401 citations recorded by the source corpus.
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 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.
Subfields: Biophysics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/8c4755f65bd678d1d3b16b8cdc7081bca35e41ca
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In Molecular Biology
- Florian P. Breitwieser
- Steven L. Salzberg
- Jennifer Lu
- Ben Langmead
- Derrick E. Wood
- Martin Steinegger
- Heng Li
- Natalia Rincon
Citations in the corpus
- Metagenome analysis using the Kraken software suite (2022, background): “The Kraken report file outputs lines containing six tab-delimited fields: (1) percentage of fragments covered by the clade rooted at this taxon, (2) number of fragments covered by the clade rooted at this taxon, (3) number of fragments assigned directly to this taxon, (4) rank code such as S for spe”