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.
