How To Install pbgenomicconsensus on Ubuntu 18.04
Introduction
In this tutorial we learn how to install pbgenomicconsensus on Ubuntu 18.04.
What is pbgenomicconsensus
pbgenomicconsensus is:
The GenomicConsensus package provides Quiver, Pacific Biosciences' flagship consensus and variant caller. Quiver is an algorithm that finds the maximum likelihood template sequence given PacBio reads of the template. These reads are modeled using a conditional random field approach that prescribes a probability to a read given a template sequence. In addition to the base sequence of each read, Quiver uses several additional quality value covariates that the base caller provides.
This package is part of the SMRTAnalysis suite
There are three methods to install pbgenomicconsensus on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install pbgenomicconsensus Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install pbgenomicconsensus using apt-get by running the following command:
sudo apt-get -y install pbgenomicconsensus
Install pbgenomicconsensus Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pbgenomicconsensus using apt by running the following command:
sudo apt -y install pbgenomicconsensus
Install pbgenomicconsensus 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 pbgenomicconsensus using aptitude by running the following command:
sudo aptitude -y install pbgenomicconsensus
How To Uninstall pbgenomicconsensus on Ubuntu 18.04
To uninstall only the pbgenomicconsensus package we can use the following command:
sudo apt-get remove pbgenomicconsensus
Uninstall pbgenomicconsensus And Its Dependencies
To uninstall pbgenomicconsensus and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove pbgenomicconsensus
Remove pbgenomicconsensus Configurations and Data
To remove pbgenomicconsensus configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge pbgenomicconsensus
Remove pbgenomicconsensus configuration, data, and all of its dependencies
We can use the following command to remove pbgenomicconsensus configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pbgenomicconsensus
References
Summary
In this tutorial we learn how to install pbgenomicconsensus package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
