How To Install yaha on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 441 words
Introduction
In this tutorial we learn how to install yaha on Ubuntu.
What is yaha
yaha is:
yaha is an open source, flexible, sensitive and accurate DNA aligner designed for single-end reads. It supports three major modes of operation:
- The default “Optimal Query Coverage” (-OQC) mode reports the best set of alignments that cover the length of each query.
- Using “Filter By Similarity” (-FBS), along with the best set of alignments, yaha will also output alignments that are highly similar to an alignment in the best set.
- Finally, yaha can output all the alignments found for each query. The -OQC and -FBS modes are specifically tuned to form split read mappings that can be used to accurately identify structural variation events (deletions, duplications, insertions or inversions) between the subject query and the reference genome.
There are three methods to install yaha 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 yaha Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install yaha using apt-get by running the following command:
sudo apt-get -y install yaha
Install yaha Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install yaha using apt by running the following command:
sudo apt -y install yaha
Install yaha 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 yaha using aptitude by running the following command:
sudo aptitude -y install yaha
How To Uninstall yaha on Ubuntu
To uninstall only the yaha package we can use the following command:
sudo apt-get remove yaha
Uninstall yaha And Its Dependencies
To uninstall yaha and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove yaha
Remove yaha Configurations and Data
To remove yaha configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge yaha
Remove yaha configuration, data, and all of its dependencies
We can use the following command to remove yaha configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge yaha
Dependencies
yaha have the following dependencies:
References
Summary
In this tutorial we learn how to install yaha package on Ubuntu using different package management tools: apt, apt-get and aptitude.