How To Install seqtk on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 385 words
Introduction
In this tutorial we learn how to install seqtk on Ubuntu.
What is seqtk
seqtk is:
Currently, seqtk supports quality based trimming with the phred algorithm, converting fastq to fasta, reverse complementing sequences, extracting or masking subsequences in regions given in a BED/name list file, and more. It contains a subsampling module to sample exactly n sequences or a fraction of sequences.
Seqtk supports both fasta and fastq input files, which can be optionally gzip compressed.
There are three methods to install seqtk 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 seqtk Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install seqtk using apt-get by running the following command:
sudo apt-get -y install seqtk
Install seqtk Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install seqtk using apt by running the following command:
sudo apt -y install seqtk
Install seqtk 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 seqtk using aptitude by running the following command:
sudo aptitude -y install seqtk
How To Uninstall seqtk on Ubuntu
To uninstall only the seqtk package we can use the following command:
sudo apt-get remove seqtk
Uninstall seqtk And Its Dependencies
To uninstall seqtk and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove seqtk
Remove seqtk Configurations and Data
To remove seqtk configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge seqtk
Remove seqtk configuration, data, and all of its dependencies
We can use the following command to remove seqtk configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge seqtk
Dependencies
seqtk have the following dependencies:
References
Summary
In this tutorial we learn how to install seqtk package on Ubuntu using different package management tools: apt, apt-get and aptitude.