How To Install skewer on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 403 words
Introduction
In this tutorial we learn how to install skewer on Ubuntu.
What is skewer
skewer is:
skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.
Features
- Detection and removal of adapter sequences
- Insertion and deletion allowed in pattern matching
- Targeted at Single End, Paired End (PE), and Long Mate Pair (LMP) reads
- Demultiplexing of barcoded sequencing runs
- Multi-threading support
- Trimming based on phred quality scores
- IUPAC characters for barcodes and adapters
- Compressed input and output support
There are three methods to install skewer on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install skewer Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install skewer using apt-get by running the following command:
sudo apt-get -y install skewer
Install skewer Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install skewer using apt by running the following command:
sudo apt -y install skewer
Install skewer 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 skewer using aptitude by running the following command:
sudo aptitude -y install skewer
How To Uninstall skewer on Ubuntu
To uninstall only the skewer package we can use the following command:
sudo apt-get remove skewer
Uninstall skewer And Its Dependencies
To uninstall skewer and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove skewer
Remove skewer Configurations and Data
To remove skewer configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge skewer
Remove skewer configuration, data, and all of its dependencies
We can use the following command to remove skewer configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge skewer
Dependencies
skewer have the following dependencies:
References
Summary
In this tutorial we learn how to install skewer package on Ubuntu using different package management tools: apt, apt-get and aptitude.