fastqc command not found

In this troubleshooting guide we learn how to fix fastqc command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

fastqc: command not found

or when using sudo you get the following error message

sudo: fastqc: command not found

Solutions to fastqc: command not found

How To Fix fastqc: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu fastqc is provided by fastqc package.

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

To fix this problem, we can install more using the command below.

sudo apt-get -y install fastqc

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install fastqc.

sudo apt -y install fastqc

Or if you have aptitude installed you can use the following command.

sudo aptitude install fastqc

Summary

In this tutorial we learn how to fix fastqc command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.