How To Install trimmomatic on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 495 words
Introduction
In this tutorial we learn how to install trimmomatic on Ubuntu.
What is trimmomatic
trimmomatic is:
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
The current trimming steps are:
- ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.
- SLIDINGWINDOW: Perform a sliding window trimming, cutting once thes average quality within the window falls below a threshold.
- LEADING: Cut bases off the start of a read, if below a threshold quality
- TRAILING: Cut bases off the end of a read, if below a threshold quality
- CROP: Cut the read to a specified length
- HEADCROP: Cut the specified number of bases from the start of the read
- MINLENGTH: Drop the read if it is below a specified length
- TOPHRED33: Convert quality scores to Phred-33
- TOPHRED64: Convert quality scores to Phred-64 It works with FASTQ (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp’ed FASTQ. Use of gzip format is determined based on the .gz extension.
There are three methods to install trimmomatic 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 trimmomatic Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install trimmomatic using apt-get by running the following command:
sudo apt-get -y install trimmomatic
Install trimmomatic Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install trimmomatic using apt by running the following command:
sudo apt -y install trimmomatic
Install trimmomatic 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 trimmomatic using aptitude by running the following command:
sudo aptitude -y install trimmomatic
How To Uninstall trimmomatic on Ubuntu
To uninstall only the trimmomatic package we can use the following command:
sudo apt-get remove trimmomatic
Uninstall trimmomatic And Its Dependencies
To uninstall trimmomatic and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove trimmomatic
Remove trimmomatic Configurations and Data
To remove trimmomatic configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge trimmomatic
Remove trimmomatic configuration, data, and all of its dependencies
We can use the following command to remove trimmomatic configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge trimmomatic
Dependencies
trimmomatic have the following dependencies:
References
Summary
In this tutorial we learn how to install trimmomatic package on Ubuntu using different package management tools: apt, apt-get and aptitude.