How To Install fastqc on Kali Linux

In this tutorial we learn how to install fastqc on Kali Linux. fastqc is quality control for high throughput sequence data

Introduction

In this tutorial we learn how to install fastqc on Kali Linux.

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 Kali Linux. 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 on Kali Linux first since aptitude is usually not installed by default on Kali Linux. 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 Kali Linux

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 Kali Linux, we can use the command below:

sudo apt-get -y autoremove fastqc

Remove fastqc Configurations and Data

To remove fastqc configuration and data from Kali Linux 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 Kali Linux using different package management tools: apt, apt-get and aptitude.