Pavian is a tool for interactive analysis of metagenomics classification results. Read more about it in the Preprint or its vignette. It's built on R and Shiny, and supports Kraken, Centrifuge and MetaPhlAn report files. Please note that currently the default Centrifuge report format is not supported. To generate a compatible report, use the script centrifuge-kreport that is distributed with Centrifuge.

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The alignment viewer requires a BAM alignment file and BAI index. To generate a BAM file, download a genome of interest, and align to it with an aligner like Bowtie2 or bwa mem. The resulting SAM file can be compressed into a binary BAM file and indexed with samtools.

Pavian metagenomics data explorer

This tool was developed by Florian Breitwieser in Steven Salzberg's lab at the Center for Computational Biology at Johns Hopkins Medical Institution. This work was supported by the U.S. National Institutes of Health [R01-HG006677,R01-GM083873]; and by the U.S. Army Research Office [W911NF-1410490].

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