PanExplorer

Web application to explore bacterial pangenomes

Homepage:: https://panexplorer.southgreen.fr

Dependencies:

• singularity
• java

Introduction

PanExplorer performs pan-genome analysis (using PGAP or Roary) and exposes resulting information as a comprehensive and easy way, through several modules facilitating the exploration gene clusters and interpretation of data.

The application allows interactive data exploration at different levels :

(i) Pan-genome visualizations as a presence/absence heatmap. This overview allows to easily identify and distinguish core-genes (present in all strains), cloud genes (genes from the accessory genome) and genome-specific genes.

(ii) Physical map of core-genes and strain-specific genes can be displayed as a circular genomic representation (Circos), for each genome taken independently.

(iii) Synteny analysis. The conservation of gene order between genomes can be investigated using graphical representations.

(iv) Visual inspection of a specific cluster.

Citation

https://doi.org/10.1093/bioinformatics/btac504

Authors

• Alexis Dereeper (IRD)
• Damien Meyer (Cirad)

Install

1- Git clone

git clone https://github.com/SouthGreenPlatform/PanExplorer.git
cd PanExplorer

2- Get the singularity container

cd singularity
wget https://panexplorer.southgreen.fr/singularity/panexplorer.sif

Run the workflow as command line

1- Define the PANEX_PATH environnement variable

export PANEX_PATH=/usr/local/bin/PanExplorer_workflow

2- Prepare your input dataset (list of genomes to be analyzed)

Edit a new file names "genbank_ids" listing the Genbank identifiers of complete assembled and annotated genomes.

The file should look like this

cat genbank_ids
CP000235.1
CP001079.1
CP001759.1
CP015994.2

3- Run the workflow

This step assumes you have singularity installed.

If singularity is not installed, have a look first to this: https://singularity-tutorial.github.io/01-installation/

Creating a pangenome using Roary

singularity exec PanExplorer/singularity/panexplorer.sif snakemake --cores 1 -s $PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG

Creating a pangenome using PGAP

singularity exec PanExplorer/singularity/panexplorer.sif snakemake --cores 1 -s $PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG

In both cases, you should a new directory named "outputs" containing all output files.

This includes:

UpsetR Diagram

Presence/absence heatmap of accessory genes:

Run the dash Web application

This section describes how to run the dash web application, allowing to interactively explore results of PanExplorer workflow

Edit the configuration to indicate the path to the data directory dash/panexplorer_config.yaml

Run the application in debug mode

cd dash
python app.py

Open the following URL: http://localhost:8050

You should obtain the following rendering

Deploy the Web application

This section describes how to deploy the web application on a Ubuntu running with Apache2.

As an example, we assume that files will be placed as follows in the following folder /var/www

1- Copy your panexplorer folder into /var/www

sudo mkdir /var/www/panexplorer
sudo cp -rf PanExplorer/* /var/www/panexplorer

2- Configure Apache

In ubuntu, the CGI module must be first enabled using this command

sudo a2enmod cgid

Add the following lines in the Apache configuration file /etc/apache2/apache2.conf or create a new VirtualHost containinf the following lines

        DocumentRoot /var/www/panexplorer/htdocs
        Alias   /panexplorer /var/www/panexplorer/htdocs

        <Directory "/var/www/panexplorer/htdocs/">
                AllowOverride All
                Options +FollowSymLinks +Indexes
                Require all granted
        </Directory>

        LoadModule cgid_module modules/mod_cgid.so

        ScriptAlias /cgi-bin/ /var/www/panexplorer/cgi-bin/

        <Directory "/var/www/panexplorer/cgi-bin/">

                Options +Indexes +FollowSymLinks +MultiViews +Includes +ExecCGI
                AllowOverride All
                SetHandler cgi-script
                Require all granted
        </Directory>
        

Restart apache

systemctl restart apache2

3- Install Perl modules

sudo perl -MCPAN -e shell

>install CGI::Session
>install MIME::Lite

4- Copy directories into dedicated HTML and CGI directories

sudo chown -R www-data /var/www/panexplorer/*
sudo chmod -R 755 /var/www/panexplorer/*

sudo chown -R www-data /var/www/panexplorer/cgi-bin/*
sudo chmod -R 755 /var/www/panexplorer/cgi-bin/*

Create a directory for storing temporary outputs

sudo mkdir /var/www/panexplorer/htdocs/tmp
sudo chown -R www-data /var/www/panexplorer/htdocs/tmp

5- Edit the Configuration file and javascript

sudo vi /var/www/panexplorer/cgi-bin/Config/Configuration.pm

Modify the following lines depending on your environnement

our $HOMEPAGE = "http://localhost/panexplorer";
our $WEB_DIR = "http://localhost/panexplorer";
our $HOME_DIR = "/var/www/panexplorer/htdocs/";
our $CGI_DIR = "/var/www/panexplorer/cgi-bin/";
our $CGI_WEB_DIR    = "http://localhost/cgi-bin";
our $TEMP_EXECUTION_DIR = "/var/www/panexplorer/htdocs/tmp";

6- Access to your application using the URL defined in Configuration.pm

http://localhost/cgi-bin/home.cgi

License

GNU General Public GPLv3 License.