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Pavian specifications


Unique identifier OMICS_13953
Name Pavian
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes




No version available



  • person_outline Florian Breitwieser

Publication for Pavian

Pavian citations


Impact of sequencing depth on the characterization of the microbiome and resistome

Sci Rep
PMCID: 5897366
PMID: 29651035
DOI: 10.1038/s41598-018-24280-8
call_split See protocol

[…] For microbiome comparisons among datasets at various sequencing depths, reads for all eukaryotes and Enterobacteria phage PhiX174 sensu lato were filtered out from the Kraken reports with Pavian. Complete taxonomic lineages were also added by Pavian. Sets of unique taxa at each sequencing depth were determined for each taxonomic level (i.e. phylum, class, family, order, genus, and spec […]


Metaviz: interactive statistical and visual analysis of metagenomic data

Nucleic Acids Res
PMCID: 5887897
PMID: 29529268
DOI: 10.1093/nar/gky136

[…] lication that computes statistical metagenomic analyses, visualizes results and is integrated with different Bioconductor packages []. Pavian is an R package that incorporates Shiny and D3.js () components to enable interactive analysis of results for metagenomic classification tools []. Panviz is a tool […]


Efficacy of an Optimised Bacteriophage Cocktail to Clear Clostridium difficile in a Batch Fermentation Model

PMCID: 5872124
PMID: 29438355
DOI: 10.3390/antibiotics7010013
call_split See protocol

[…] were trimmed with Sickle using default parameters, and metagenomes were assembled using megahit. An overview of sample diversity for each metagenome was obtained using Kraken [] and visualised using Pavian []. The reads were mapped against the genomes of interest using BWA-MEM []). […]


Identifying Corneal Infections in Formalin Fixed Specimens Using Next Generation Sequencing

PMCID: 5770184
PMID: 29340642
DOI: 10.1167/iovs.17-21617
call_split See protocol

[…] ired 75-base pair (bp) reads; that is, 150 bases per DNA fragment. The read pairs were analyzed with two different metagenomics classification engines, Kraken and Centrifuge, and visualized using the Pavian software tool (; ). The reads from each group were analyzed by a bioinformatics team (FPB, JL, SLS) who were masked with respect to pathology and microbiology diagnostic data until after report […]


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Pavian institution(s)
Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Departments of Biomedical Engineering and Biostatistics, Johns Hopkins University, Baltimore, MD, USA
Pavian funding source(s)
This research was supported in part by NIH under grants R01 HG006677 and R01 GM083873, and by the U. S. Army Research Office under grant W911NF-14-1-0490.

Pavian review

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Anonymous user #4386

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Awesome way to further analyze or just visualize Kraken results.