How To Install fastqc on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 448 words
Introduction
In this tutorial we learn how to install fastqc on Ubuntu.
What is fastqc
fastqc is:
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
The main functions of FastQC are
- Import of data from BAM, SAM or FastQ files (any variant)
- Providing a quick overview to tell you in which areas there may be problems
- Summary graphs and tables to quickly assess your data
- Export of results to an HTML based permanent report
- Offline operation to allow automated generation of reports without running the interactive application
There are three methods to install fastqc on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install fastqc Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install fastqc using apt-get by running the following command:
sudo apt-get -y install fastqc
Install fastqc Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install fastqc using apt by running the following command:
sudo apt -y install fastqc
Install fastqc Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install fastqc using aptitude by running the following command:
sudo aptitude -y install fastqc
How To Uninstall fastqc on Ubuntu
To uninstall only the fastqc package we can use the following command:
sudo apt-get remove fastqc
Uninstall fastqc And Its Dependencies
To uninstall fastqc and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove fastqc
Remove fastqc Configurations and Data
To remove fastqc configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge fastqc
Remove fastqc configuration, data, and all of its dependencies
We can use the following command to remove fastqc configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge fastqc
Dependencies
fastqc have the following dependencies:
References
Summary
In this tutorial we learn how to install fastqc package on Ubuntu using different package management tools: apt, apt-get and aptitude.