Pavian 1.2.0

Pavian - interactive browser application for omics data

Pavian is a interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, KrakenUniq, Kraken 2, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome.

Location and version:

1
2
3
4

$ bash
$ source /local/cluster/pavian/activate.sh
$ Rscript -e "packageVersion('pavian')"
[1] ‘1.2.0’

A wrapper script has been provided to facilitate the use of interactive pavian sessions.

On vaughan:

1
2

cd /path/to/viz/dir
SGE_Batch -c 'start_pavian' -q <QUEUE> -r sge.pavian

Examine the stdout in the sge.pavian directory to get the ssh command to run for the port tunneling to the node, then navigate your local browser to the given url to get started. By default, the ‘load dataset’ tab should be in your current working directory.

Make sure to kill the job using qdel when you are finished with your session.

To close the tunneled connection from your local machine, run the ssh -S <SOCKET_NAME> -O check . and ssh -S <SOCKET_NAME> -O exit . commands as given. You can check for already established sockets by running ls $HOME/.ssh and looking for files named <HOST>-<PORT>-pavian.

software ref: https://github.com/fbreitwieser/pavian
research ref: https://doi.org/10.1093/bioinformatics/btz715