How To Install art-nextgen-simulation-tools on Ubuntu 22.04

In this tutorial we learn how to install art-nextgen-simulation-tools on Ubuntu 22.04. art-nextgen-simulation-tools is simulation tools to generate synthetic next-generation sequencing reads

Introduction

In this tutorial we learn how to install art-nextgen-simulation-tools on Ubuntu 22.04.

What is art-nextgen-simulation-tools

art-nextgen-simulation-tools is:

ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina’s Solexa, Roche’s 454 and Applied Biosystems’ SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. ART can be used together with genome variants simulators (e.g. VarSim) for evaluating variant calling tools or methods.

There are three methods to install art-nextgen-simulation-tools 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 art-nextgen-simulation-tools Using apt-get

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

sudo apt-get update

After updating apt database, We can install art-nextgen-simulation-tools using apt-get by running the following command:

sudo apt-get -y install art-nextgen-simulation-tools

Install art-nextgen-simulation-tools Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install art-nextgen-simulation-tools using apt by running the following command:

sudo apt -y install art-nextgen-simulation-tools

Install art-nextgen-simulation-tools 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 art-nextgen-simulation-tools using aptitude by running the following command:

sudo aptitude -y install art-nextgen-simulation-tools

How To Uninstall art-nextgen-simulation-tools on Ubuntu 22.04

To uninstall only the art-nextgen-simulation-tools package we can use the following command:

sudo apt-get remove art-nextgen-simulation-tools

Uninstall art-nextgen-simulation-tools And Its Dependencies

To uninstall art-nextgen-simulation-tools and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:

sudo apt-get -y autoremove art-nextgen-simulation-tools

Remove art-nextgen-simulation-tools Configurations and Data

To remove art-nextgen-simulation-tools configuration and data from Ubuntu 22.04 we can use the following command:

sudo apt-get -y purge art-nextgen-simulation-tools

Remove art-nextgen-simulation-tools configuration, data, and all of its dependencies

We can use the following command to remove art-nextgen-simulation-tools configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge art-nextgen-simulation-tools

References

Summary

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