How To Install plasmidseeker on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 397 words
Introduction
In this tutorial we learn how to install plasmidseeker on Ubuntu.
What is plasmidseeker
plasmidseeker is:
PlasmidSeeker is a k-mer based program for the identification of known plasmids from bacterial whole genome sequencing reads.
PlasmidSeeker that enables the detection of plasmids from bacterial WGS data without read assembly. The PlasmidSeeker algorithm is based on k-mers and uses k-mer abundance to distinguish between plasmid and bacterial sequences. The performance of PlasmidSeeker was tested on a set of simulated and real bacterial WGS samples, resulting in 100% sensitivity and 99.98% specificity.
There are three methods to install plasmidseeker 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 plasmidseeker Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install plasmidseeker using apt-get by running the following command:
sudo apt-get -y install plasmidseeker
Install plasmidseeker Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install plasmidseeker using apt by running the following command:
sudo apt -y install plasmidseeker
Install plasmidseeker 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 plasmidseeker using aptitude by running the following command:
sudo aptitude -y install plasmidseeker
How To Uninstall plasmidseeker on Ubuntu
To uninstall only the plasmidseeker package we can use the following command:
sudo apt-get remove plasmidseeker
Uninstall plasmidseeker And Its Dependencies
To uninstall plasmidseeker and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove plasmidseeker
Remove plasmidseeker Configurations and Data
To remove plasmidseeker configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge plasmidseeker
Remove plasmidseeker configuration, data, and all of its dependencies
We can use the following command to remove plasmidseeker configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge plasmidseeker
Dependencies
plasmidseeker have the following dependencies:
References
Summary
In this tutorial we learn how to install plasmidseeker package on Ubuntu using different package management tools: apt, apt-get and aptitude.