Install SRA toolkit

SRA toolkit contains important tools to manipulate SRA (Short Read Archive) file.

The objective of this article is to show you, how to install SRA toolkit on Ubuntu/Linux system.


Installation



1. Download the last version for your computer operating system from here

Use the following command on Linux to download the file sratoolkit.2.4.1-ubuntu64.tar.gz:

Code BASH :
 
#Download the file for ubuntu system
wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.4.1/sratoolkit.2.4.1-ubuntu64.tar.gz
# Unzip the archive
tar xzvf sratoolkit.2.4.1-ubuntu64.tar.gz
 



2. Modify your .bashrc file so that when you type "fastq-dump" , for example, it calls the program:
Code BASH :
export PATH=$PATH:/directory/sratoolkit.2.4.1-ubuntu64/bin



Directory is equal to the directory that you have installed sratoolkit in. Example:
Code BASH :
export PATH=$PATH:/home/kassambara/Documents/sequencing/tools/sratoolkit.2.4.1-ubuntu64/bin


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