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

Access to Document

10.1093/bioinformatics/btz715

Fingerprint Dive into the research topics of 'Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification'. Together they form a unique fingerprint.

Cite this

@article{c908e540f7e341e6915832830e3186ca,

title = "Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification",

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.}",

year = "2020",

month = feb,

day = "15",

doi = "10.1093/bioinformatics/btz715",

language = "English (US)",

volume = "36",

pages = "1303--1304",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "4",

}

TY - JOUR

T1 - Pavian

T2 - Interactive analysis of metagenomics data for microbiome studies and pathogen identification

AU - Breitwieser, Florian P.

AU - Salzberg, Steven L.

PY - 2020/2/15

Y1 - 2020/2/15

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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85080845812&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85080845812&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btz715

DO - 10.1093/bioinformatics/btz715

M3 - Article

C2 - 31553437

AN - SCOPUS:85080845812

VL - 36

SP - 1303

EP - 1304

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 4

ER -