Rhinovirus Viewer 🦏🦠

Rhinovirus Viewer is a web-based tool for visualizing rhinovirus genomic data using JBrowse2. After installation, this tool allows users to explore and analyze rhinovirus genomes and related data.

Features

• Visualize rhinovirus genomic data
• Explore rhinovirus A, B, and C strains
• Integrated with JBrowse2 for advanced genomic visualization
• Expandable installation script to allow for addition of genome assemblies. Modify scripts in installation/ to do so

Installation Options

Option 1: Use the GitHub Pages Website

You can simply use the Rhinovirus Viewer hosted on GitHub Pages:

• Rhinovirus Viewer: atamadon.github.io
• JBrowse2 Instance: atamadon.github.io/jbrowse2

Option 2: Install on Debian/Ubuntu Based Linux Distribution

Follow these steps to install and set up Rhinovirus Viewer on a Debian/Ubuntu based Linux distribution using the install_linux.sh script located in the installation/ directory:

1. Clone the Repository

   git clone https://github.com/atamadon/atamadon.github.io.git
   cd atamadon.github.io

2. OPTIONAL: Adding Additional Genome Assemblies

   The installation script uses a bash arrays to store FTP links to the genome FASTA files and GFF track annotations. If you wish to add additional assemblies, simply aquire the FTP links to the corresponding .fasta and .gff files and add them to the strains and tracks bash arrays respectively in installation/install_linux.sh.

3. Run the Installation Script

   chmod +x installation/install_linux.sh

   ./installation/install_linux.sh

4. Access the Viewer

   Navigate to http://your-server-ip/jbrowse2 in your web browser. Apache will output the IP address to the shell. Otherwise, run:

   ip addr show eth0 | grep "inet\b" | awk '{print $2}' | cut -d/ -f1

   To locate the server's IP address.

5. NOTE: Your milage may vary

   Please be mindful of your system's installation environment. This method is prone to dependency errors, issues with networking, and general linux file permission headaches. Use the devcontainer option for a streamlined experience.

Option 3: Use a DevContainer in Visual Studio Code (Preferred)

The preferred option is to use a DevContainer in Visual Studio Code, which automatically installs all dependencies and launches an instance of the JBrowse viewer at localhost/jbrowse2. This option only requires Docker Engine to be installed locally.

1. Install Docker Engine

   Follow the instructions to install Docker Engine on your system: Docker Installation Guide

2. Clone the Repository

   git clone https://github.com/atamadon/atamadon.github.io.git
   cd atamadon.github.io

3. Open in Visual Studio Code

   Open the project in Visual Studio Code. You should see a VSCode prompt in the bottom right to reopen the project in a DevContainer. If not, open the Command Palatte and select >Remote-Containers: Reopen in Container.

4. Run the DevContainer Setup Script

   The install_devcontainer.sh script will automatically run inside the DevContainer to install all dependencies and set up the JBrowse viewer.

5. OPTIONAL: Adding Additional Genome Assemblies

   The installation script uses a bash arrays to store FTP links to the genome FASTA files and GFF track annotations. If you wish to add additional assemblies, simply aquire the FTP links to the corresponding .fasta and .gff files and add them to the strains and tracks bash arrays respectively in installation/install_devcontainer.sh. The JBrowse instance will be updated with the new assemblies automatically the next time the container is rebuilt, or by running >Dev Containers: Rebuild.

6. Access the Viewer

   Navigate to http://localhost/jbrowse2 in your web browser.

Usage

Getting Started Once you have succefully installed JBrowse and can access your instance in a web browser, you are ready to begin exploring different rhinovirus genomes!

1. Opening JBrowse for the first time will prompt you to Start a new session.
2. Select Empty to get started.

Select a view to launch

1. JBrowse supports a number of views to view genomic data in a convienent way.
2. Linear Genome View allows for visualizing genome sequences along with their corresponding track annotations.
3. Linear Syntheny and Dotplot Views allow for visualizing pairwise sequence alignments calculated with minimap2 for each genome pair using 5 different command line arguments.
4. Multiple Sequence Alignment View allows for visualizing multiple sequence alignmnets calculated with muscle for all genomes. See information below to use the plugin.

Add the MsaView Plugin to view the alignments

1. Natigate and click on the Tools ▼ dropdown
2. Click on the Plugin Store
3. Find MsaView under the Avalible plugins and click + INSTALL
4. Once installed, nativate to the Add ▼ dropdown and select Multiple Sequence Alignment view
5. MsaView will prompt for a MSA File or URL. Select File, and choose the all_assemblies.msa.fasta file that was downloaded with the cloned git repository. Open to view.
6. MsaView will display both a visual MSA as well as a phylogenetic tree. Feel free to upload your own MSAs to view.