How To Install trim-galore on Kali Linux
Introduction
In this tutorial we learn how to install trim-galore on Kali Linux.
What is trim-galore
trim-galore is:
Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It’s main features are:
- For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters (‘AGATCGGAAGAGC’) by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too
- For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation
- For any kind of FastQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter- and quality trimming
- The Phred quality of basecalls and the stringency for adapter removal can be specified individually
- Trim Galore! can remove sequences if they become too short during the trimming process. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality
- Trim Galore! can trim paired-end files by 1 additional bp from the 3’ end of all reads to avoid problems with invalid alignments with Bowtie 1
- Trim Galore! accepts and produces standard or gzip compressed FastQ files
- FastQC can optionally be run on the resulting output files once trimming has completed
There are three methods to install trim-galore 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 trim-galore Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install trim-galore using apt-get by running the following command:
sudo apt-get -y install trim-galoreInstall trim-galore Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install trim-galore using apt by running the following command:
sudo apt -y install trim-galoreInstall trim-galore 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 updateAfter updating apt database, We can install trim-galore using aptitude by running the following command:
sudo aptitude -y install trim-galoreHow To Uninstall trim-galore on Kali Linux
To uninstall only the trim-galore package we can use the following command:
sudo apt-get remove trim-galoreUninstall trim-galore And Its Dependencies
To uninstall trim-galore and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove trim-galoreRemove trim-galore Configurations and Data
To remove trim-galore configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge trim-galoreRemove trim-galore configuration, data, and all of its dependencies
We can use the following command to remove trim-galore configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge trim-galoreDependencies
trim-galore have the following dependencies:
References
Summary
In this tutorial we learn how to install trim-galore package on Kali Linux using different package management tools: apt, apt-get and aptitude.
