NanoViZer (Nanopore Virus analyZer) is an interactive data-visualisation and chart-saver tool assisting researchers in their work.

This is a Vue.js v3 project bootstrapped with Create Vue. Backend can be found here.

See it live.

Table of contents

• Requirements
• Using NanoViZer for the first time
• Running NanoViZer

Requirements

• Git
• Python 3
• Node and npm

Using NanoViZer for the first time

1. Install dependencies

   1. Download and install Git

   2. Download and install Python

   3. Download and install npm

2. Set up the project

   1. Go where you want the NanoViZer repository to be installed to

   2. Set up the backend of NanoViZer

      1. Clone the repository

         git clone https://github.com/CorentinAube/NanoViZer.git

      2. Go to the newly created nanovizer folder

      3. Open a terminal and install the dependencies

         apt-get update -y && apt-get install -y python3-pip python-dev bedtools && pip3 install Flask Flask-Cors

   3. Set up the frontend of NanoViZer

      1. Return to where the NanoViZer repository is installed

      2. Clone the repository

         git clone https://github.com/Benjent/nanovizer.git

      3. Go to the newly created nanovizer-front folder

      4. Open a terminal and install the dependencies

         npm install

3. Follow the steps in the Running NanoViZer section

Running NanoViZer

1. Run the project

   • Using the vanilla method

     1. Run the backend in a terminal

        app.py

     2. Run the frontend in another terminal

        npm run dev

   • Using the custom method

     python3 app.py

2. Open a browser tab and go to the following URL

   http://localhost:3000/

3. Put the .bam file in the /data folder

Theme and contrast

You can switch from dark to light themes with the button on the top-right corner of the screen. You can also increase the contrast with the button next to it.

💡 Tip Use the light theme along with high contrast to obtain black on white charts, that you can save as is, which is handful for print purpose.

FAQ

What is the reason for this repository?

There is an existing NanoViZer backend solution, coded in Python, which generates several charts with a given .bam file. This repository allows the same charts to be generated through a frontend solution, except they are now interactive, and without re-writing the existing NanoViZer code.

How to open a terminal?

Inside the file explorer, right click and click on Git bash here.

Why not using a serverless app?

• This project is intended to run for free
• .bam files are too heavy to manipulate for free (some of them exceed 100GB)
• It is faster to move .bam files in a local directory compared to uploading them in the cloud