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.

For help and more documenation please go to https://github.com/fbreitwieser/pavian.

Upload metagenomics report files from the local computer. If selecting multiple files does not work, please try with a different browser. With each sample set, you may also include meta-data with a colon-separated sample_data.csv file that has at least the columns 'Name' and 'ReportFile'.
Two example datasets are available: brain-biopsies and hmp-stool. The first set is from ten patients with suspected infections of the nervous system, analyzed with Kraken. The second set is sequenced stool from the Human Microbiome Project, analyzed with MetaPhlAn. Note that for MetaPhlAn, the values are percentages/abundances rather than reads.


Instructions

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.


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Gather and display the content of the assembly_summary.txt from the selected domain from ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq. An active internet connection is required, and currently no files are cached.



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].



Session Information