All BIOM and RDF files generated by NG-Tax can easily be analysed using the NG-Tax toolbox. It is developed within a docker environment and it is therefore required to have the docker installed on the local/server machine.

Starting the toolbox

To start the NG-Tax toolbox, run the following command:

docker run --rm -p 3838:3838 wurssb/ngtaxtoolbox

First time downloading the docker image, you will see the following: dockerDownload

When the program starts, the terminal will shows the following messages:

[2018-08-27T14:48:46.565] [INFO] shiny-server - Shiny Server v1.5.8.921 (Node.js v8.11.3)
[2018-08-27T14:48:46.568] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
[2018-08-27T14:48:46.636] [WARN] shiny-server - Running as root unnecessarily is a security risk! You could be running more securely as non-root.
[2018-08-27T14:48:46.641] [INFO] shiny-server - Starting listener on http://[::]:3838
[2018-08-27T14:48:52.725] [INFO] shiny-server - Created bookmark state directory: /var/lib/shiny-server/bookmarks
[2018-08-27T14:48:52.726] [INFO] shiny-server - Created user bookmark state directory: /var/lib/shiny-server/bookmarks/shiny



Accessing the toolbox

When the previous command is executed on a local machine, the toolbox is available through the browser at http://localhost:3838/

If it starts on the server, it can often be accessed via http://<hostname>:3838. The “hostname” can often be identified by typing “hostname” in the command line interface.

When the url is visited, you should see the following interface:

Here you can drag and drop your BIOM/RDF file in the green panel and press “Start the analysis”.

Data Analysis

After the data is uploaded and converted, the tab will automatically switch to “Data overview” under Data Analysis" menu.

Data overview



ASV information

This section contains information about the taxomonic classification and it corresponding read count.



Species composition analysis

This section contains an illustration of the microbial composition of each sample in both bar plot and heatmap.
Different resolution of the taxonomy and type of data, such as raw counts or relative abundance, can be selected for visualization.



Venn diagram

The venn diagram can represent the unique or overlapped taxonomic lineage between different sample.
Different resolution of the taxonomy can be selected for visualization.



Phylogenetic tree



Rarefraction curve



Alpha diversity



Beta diversity



SPARQL

User defined queries could be use here for further analysis. Example of queries can be found under RDF tutorial

Laboratory of Systems and Synthetic Biology - Wageningen University & Research