Pavian is a interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome.
For more information look at the preprint at http://biorxiv.org/content/early/2016/10/31/084715.full.pdf+html . Please cite the preprint if you use Pavian in your research.
You can try out Pavian at https://fbreitwieser.shinyapps.io/pavian/.
The Galaxy Branch modifies the traditional implementation of Pavian to include a modified version of R-Galaxy-Connector made specifically for Pavian
This version of Pavian was made to be a Galaxy Interactive Envrionment inside of Galaxy Project. One of the key features is that it can access your datasets and collections from your current Galaxy history. This eliminates the need for downloading and reuploading your datasets and is much quicker at accessing collections than it would be otherwise.
Pavian is an R package, and thus requires R to run. Look here for how to install R. On Windows, you probably need to install Rtools. On Ubuntu, install r-base-dev. Once you started R, the following commands will install the package:
if (!require(remotes)) { install.packages("remotes") }
remotes::install_github("phac-nml/pavian", ref='master')To run Pavian from R, type
pavian::runApp(port=5000)Pavian will then be available at http://127.0.0.1:5000 in the web browser of you choice.
Alternatively, you can install and test Pavian with the following command:
shiny::runGitHub("justinband/pavian", subdir = "inst/shinyapp")The alignment viewer uses Rsamtools. To install this package from Bioconductor, use the following commands
source("https://bioconductor.org/biocLite.R")
biocLite("Rsamtools")As an alternative to installing Pavian in R, a Docker image can be used. The Docker image for pavian in galaxy is yet to be made available. However, the image for the original pavian is available at florianbw/pavian. When you run this docker image, Pavian will start automatically on port 80, which you need to make available to the hosting machine. On the shell, you can pull the image and remap the Docker port to port 5000 with the following commands:
# Get the docker image
docker pull 'jband/pavian'
# Run the docker image
docker run --rm -p 5000:80 jband/pavian
pavian natively supports the Kraken and MetaPhlAn-style report formats. In extension, you can use Centrifuge results by running centrifuge-kreport on Centrifuge output files, and Kaiju results by running kraken-report on Kaiju output files (see issue #11)
Originally, pavian's read_server_directory can only read directories with <= 100 files. I have increased this size to 300 to allow for larger collections of data to be passed through. Still, keep in mind a larger collection will load slower than a smaller collection.
The maximum upload size is defined by the option shiny.maxRequestSize. To increase it to 500 MB, for example, type the following before pavian::runApp():
options(shiny.maxRequestSize=500*1024^2)If your BAM file contains the unaligned reads, you can decrease the file size before uploading by getting rid of non-aligned reads using samtools view -F4.