How To Install fastx-toolkit on Ubuntu 18.04
Introduction
In this tutorial we learn how to install fastx-toolkit on Ubuntu 18.04.
What is fastx-toolkit
fastx-toolkit is:
The FASTX-Toolkit is a collection of command line tools for preprocessing short nucleotide reads in FASTA and FASTQ formats, usually produced by Next-Generation sequencing machines. The main processing of such FASTA/FASTQ files is mapping (aligning) the sequences to reference genomes or other databases using specialized programs like BWA, Bowtie and many others. However, it is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome—manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks.
There are three methods to install fastx-toolkit on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install fastx-toolkit Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install fastx-toolkit using apt-get by running the following command:
sudo apt-get -y install fastx-toolkit
Install fastx-toolkit Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install fastx-toolkit using apt by running the following command:
sudo apt -y install fastx-toolkit
Install fastx-toolkit 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 fastx-toolkit using aptitude by running the following command:
sudo aptitude -y install fastx-toolkit
How To Uninstall fastx-toolkit on Ubuntu 18.04
To uninstall only the fastx-toolkit package we can use the following command:
sudo apt-get remove fastx-toolkit
Uninstall fastx-toolkit And Its Dependencies
To uninstall fastx-toolkit and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove fastx-toolkit
Remove fastx-toolkit Configurations and Data
To remove fastx-toolkit configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge fastx-toolkit
Remove fastx-toolkit configuration, data, and all of its dependencies
We can use the following command to remove fastx-toolkit configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge fastx-toolkit
References
Summary
In this tutorial we learn how to install fastx-toolkit package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
