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 http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2

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.

References

1. Gordon, A., & Hannon, G. J. (2010). Fastx-toolkit. FASTQ/A short-reads preprocessing tools (unpublished) http://hannonlab. cshl. edu/fastx_toolkit, 5.