How To Install cutesv on Ubuntu 22.04

In this tutorial we learn how to install cutesv on Ubuntu 22.04. cutesv is comprehensive discovery of structural variations of genomic sequences

Introduction

In this tutorial we learn how to install cutesv on Ubuntu 22.04.

What is cutesv

cutesv is:

Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads.

cuteSV is a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.

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

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

sudo apt-get update

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

sudo apt-get -y install cutesv

Install cutesv Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install cutesv

Install cutesv 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 cutesv using aptitude by running the following command:

sudo aptitude -y install cutesv

How To Uninstall cutesv on Ubuntu 22.04

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

sudo apt-get remove cutesv

Uninstall cutesv And Its Dependencies

To uninstall cutesv and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:

sudo apt-get -y autoremove cutesv

Remove cutesv Configurations and Data

To remove cutesv configuration and data from Ubuntu 22.04 we can use the following command:

sudo apt-get -y purge cutesv

Remove cutesv configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge cutesv

References

Summary

In this tutorial we learn how to install cutesv package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.