How To Install yaha on Ubuntu 22.04
Introduction
In this tutorial we learn how to install yaha
on Ubuntu 22.04.
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 22.04. 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 22.04
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 22.04, 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 22.04 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
References
Summary
In this tutorial we learn how to install yaha
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.