How To Install yanagiba on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 398 words
Introduction
In this tutorial we learn how to install yanagiba on Ubuntu.
What is yanagiba
yanagiba is:
Yanagiba is used to filter short or low quality Oxford Nanopore reads which have been basecalled with Albacore. It takes fastq.gz and an Albacore summary file as input. If no Albacore summary file is provided attempt to calculate mean qscore from directly from fastq file using NanoMath. Note: Calculated quality scores appear to be lower for reads called with Metrichor, you may need to lower your minqual setting in this case.
There are three methods to install yanagiba 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 yanagiba Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install yanagiba using apt-get by running the following command:
sudo apt-get -y install yanagiba
Install yanagiba Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install yanagiba using apt by running the following command:
sudo apt -y install yanagiba
Install yanagiba 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 yanagiba using aptitude by running the following command:
sudo aptitude -y install yanagiba
How To Uninstall yanagiba on Ubuntu
To uninstall only the yanagiba package we can use the following command:
sudo apt-get remove yanagiba
Uninstall yanagiba And Its Dependencies
To uninstall yanagiba and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove yanagiba
Remove yanagiba Configurations and Data
To remove yanagiba configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge yanagiba
Remove yanagiba configuration, data, and all of its dependencies
We can use the following command to remove yanagiba configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge yanagiba
Dependencies
yanagiba have the following dependencies:
References
Summary
In this tutorial we learn how to install yanagiba package on Ubuntu using different package management tools: apt, apt-get and aptitude.