How To Install trimmomatic on Kali Linux

In this tutorial we learn how to install trimmomatic on Kali Linux. trimmomatic is flexible read trimming tool for Illumina NGS data

Introduction

In this tutorial we learn how to install trimmomatic on Kali Linux.

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 Kali Linux. 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 on Kali Linux first since aptitude is usually not installed by default on Kali Linux. 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 Kali Linux

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 Kali Linux, we can use the command below:

sudo apt-get -y autoremove trimmomatic

Remove trimmomatic Configurations and Data

To remove trimmomatic configuration and data from Kali Linux 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 Kali Linux using different package management tools: apt, apt-get and aptitude.