Installing FASTX-toolkit on Ubuntu

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Installing FASTX-toolkit on Ubuntu

FASTX-toolkit is a command-line bioinformatics software package for the preprocessing of short reads FASTQ/A files [1]. These files contain multiple short-read sequences obtained as an output of next-generation sequencing. In this article, we are going to install FASTX-toolkit on Ubuntu.

Getting started

Let’s update and upgrade the system first.

Open the terminal (Ctrl+T) and type the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading FASTX-toolkit

Change to the directory where you wish to download the software.

$ cd Downloads/

Make a new directory named “fastx-toolkit” where we will install the binaries.

$ mkdir fastx_toolkit

Move inside this directory and download the toolkit. You can either download it from here or use the following command:

$ cd fastx_toolkit/

$ wget

Now extract the downloaded archive file using the following commands:

$ tar xvf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2

You will be able to see the binaries.  Now, add these binaries to your path.

$ sudo cp ./bin/* /usr/local/bin

Now, you can easily use all the binaries from the terminal by entering their names.


  1. Gordon, A., & Hannon, G. J. (2010). Fastx-toolkit. FASTQ/A short-reads preprocessing tools (unpublished) http://hannonlab. cshl. edu/fastx_toolkit5.
Tariq is founder of Bioinformatics Review and a professional Software Developer at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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