How To Install sickle on Ubuntu 18.04
Introduction
In this tutorial we learn how to install sickle on Ubuntu 18.04.
What is sickle
sickle is:
Most modern sequencing technologies produce reads that have deteriorating quality towards the 3’-end. Incorrectly called bases here negatively impact assembles, mapping, and downstream bioinformatics analyses.
Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3’-end of reads. It will also discard reads based upon the length threshold. It takes the quality values and slides a window across them whose length is 0.1 times the length of the read. If this length is less than 1, then the window is set to be equal to the length of the read. Otherwise, the window slides along the quality values until the average quality in the window drops below the threshold. At that point the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there. However, if the cut point is less than the minimum length threshold, then the read is discarded entirely.
Sickle supports four types of quality values: Illumina, Solexa, Phred, and Sanger. Note that the Solexa quality setting is an approximation (the actual conversion is a non-linear transformation). The end approximation is close.
Sickle also supports gzipped file inputs.
There are three methods to install sickle 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 sickle Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install sickle using apt-get by running the following command:
sudo apt-get -y install sickle
Install sickle Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install sickle using apt by running the following command:
sudo apt -y install sickle
Install sickle 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 sickle using aptitude by running the following command:
sudo aptitude -y install sickle
How To Uninstall sickle on Ubuntu 18.04
To uninstall only the sickle package we can use the following command:
sudo apt-get remove sickle
Uninstall sickle And Its Dependencies
To uninstall sickle and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove sickle
Remove sickle Configurations and Data
To remove sickle configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge sickle
Remove sickle configuration, data, and all of its dependencies
We can use the following command to remove sickle configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge sickle
References
Summary
In this tutorial we learn how to install sickle package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
