How To Install kraken on Debian 10
Introduction
In this tutorial we learn how to install kraken on Debian 10.
What is kraken
kraken is:
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
In its fastest mode of operation, for a simulated metagenome of 100 bp reads, Kraken processed over 4 million reads per minute on a single core, over 900 times faster than Megablast and over 11 times faster than the abundance estimation program MetaPhlAn. Kraken’s accuracy is comparable with Megablast, with slightly lower sensitivity and very high precision.
There are three methods to install kraken on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install kraken Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install kraken using apt-get by running the following command:
sudo apt-get -y install kraken
Install kraken Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install kraken using apt by running the following command:
sudo apt -y install kraken
Install kraken 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 Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install kraken using aptitude by running the following command:
sudo aptitude -y install kraken
How To Uninstall kraken on Debian 10
To uninstall only the kraken package we can use the following command:
sudo apt-get remove kraken
Uninstall kraken And Its Dependencies
To uninstall kraken and its dependencies that are no longer needed by Debian 10, we can use the command below:
sudo apt-get -y autoremove kraken
Remove kraken Configurations and Data
To remove kraken configuration and data from Debian 10 we can use the following command:
sudo apt-get -y purge kraken
Remove kraken configuration, data, and all of its dependencies
We can use the following command to remove kraken configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge kraken
Dependencies
kraken have the following dependencies:
References
Summary
In this tutorial we learn how to install kraken package on Debian 10 using different package management tools: apt, apt-get and aptitude.