Install NGS on Ubuntu 20.04

March 07, 2021 2022

A guide for installing Next-Generation Sequencing (NGS) tools on Ubuntu 20.04 LTS. This post documents the steps taken during my setup process.

Installation Procedure

1. Linux (Ubuntu) Distribution

Start with a laptop or desktop running a Debian-based Linux distribution (e.g., Ubuntu 20.04 LTS).

2. Anaconda

Anaconda is a popular Python distribution that simplifies package management. While Ubuntu comes with Python by default, it’s recommended to use a modern version like Python 3.8.

Download: Visit the official Anaconda website to download the Linux installer.
Select Installer: Choose the “64-Bit (x86) Installer”.
Install: The installer will be a .sh file (e.g., Anaconda3-2020.11-Linux-x86_64.sh). Open your terminal and run:
```
bash ~/Downloads/Anaconda3-2020.11-Linux-x86_64.sh
```
Initialize: Once the installation is complete, initialize Anaconda by running:
```
conda init
```
Open Navigator (Optional): To use the graphical interface, run:
```
anaconda-navigator
```

You can find the full installation guide here.

3. SRA Tools with Bioconda

Bioconda is a channel for the conda package manager specializing in bioinformatics software. To install sra-tools, run:

conda install -c bioconda sra-tools

Note: This might install an older version. It is often recommended to specify a newer version or use a specific label if required:

conda install -c bioconda/label/cf201901 sra-tools

Refer to the Bioconda documentation for more details.

Managing Conda Environments:

Check for the (base) prompt in your terminal.
Activate: conda activate
Deactivate: conda deactivate

4. FastQC

FastQC is used for quality control checks on raw sequence data.

Prerequisite: Ensure Java is installed. Check with:
```
java -version
```
If Java is not installed, follow a guide like this one to install it.

Install FastQC: Run the following command:

sudo apt update
sudo apt install -y fastqc