How To Install qcat on Ubuntu 22.04

In this tutorial we learn how to install qcat on Ubuntu 22.04. qcat is demultiplexing Oxford Nanopore reads from FASTQ files

Introduction

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

What is qcat

qcat is:

Qcat is a command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files. It accepts basecalled FASTQ files and splits the reads into separate FASTQ files based on their barcode. Qcat makes the demultiplexing algorithms used in albacore/guppy and EPI2ME available to be used locally with FASTQ files. Currently qcat implements the EPI2ME algorithm.

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

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

sudo apt-get update

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

sudo apt-get -y install qcat

Install qcat Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install qcat

Install qcat 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 qcat using aptitude by running the following command:

sudo aptitude -y install qcat

How To Uninstall qcat on Ubuntu 22.04

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

sudo apt-get remove qcat

Uninstall qcat And Its Dependencies

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

sudo apt-get -y autoremove qcat

Remove qcat Configurations and Data

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

sudo apt-get -y purge qcat

Remove qcat configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge qcat

References

Summary

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