How To Install vg on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 462 words

Introduction

In this tutorial we learn how to install vg on Ubuntu.

What is `vg`

vg is:

variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods

Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of:

nodes, which are labeled by sequences and ids
edges, which connect two nodes via either of their respective ends
paths, describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks through nodes connected by edges

This model is similar to a number of sequence graphs that have been used in assembly and multiple sequence alignment. Paths provide coordinate systems relative to genomes encoded in the graph, allowing stable mappings to be produced even if the structure of the graph is changed.

There are three methods to install vg 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 vg Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install vg using apt-get by running the following command:

sudo apt-get -y install vg

Install vg Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install vg using apt by running the following command:

sudo apt -y install vg

Install vg 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 vg using aptitude by running the following command:

sudo aptitude -y install vg

How To Uninstall vg on Ubuntu

To uninstall only the vg package we can use the following command:

sudo apt-get remove vg

Uninstall vg And Its Dependencies

To uninstall vg and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove vg

Remove vg Configurations and Data

To remove vg configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge vg

Remove vg configuration, data, and all of its dependencies

We can use the following command to remove vg configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge vg

Dependencies

vg have the following dependencies:

References

vg website

Summary

In this tutorial we learn how to install vg package on Ubuntu using different package management tools: apt, apt-get and aptitude.