How To Install art-nextgen-simulation-tools-profiles on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 508 words
Introduction
In this tutorial we learn how to install art-nextgen-simulation-tools-profiles on Ubuntu.
What is art-nextgen-simulation-tools-profiles
art-nextgen-simulation-tools-profiles 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.
This package contains profile data for art-nextgen-simulation-tools.
There are three methods to install art-nextgen-simulation-tools-profiles 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 art-nextgen-simulation-tools-profiles 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-profiles using apt-get by running the following command:
sudo apt-get -y install art-nextgen-simulation-tools-profiles
Install art-nextgen-simulation-tools-profiles 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-profiles using apt by running the following command:
sudo apt -y install art-nextgen-simulation-tools-profiles
Install art-nextgen-simulation-tools-profiles 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-profiles using aptitude by running the following command:
sudo aptitude -y install art-nextgen-simulation-tools-profiles
How To Uninstall art-nextgen-simulation-tools-profiles on Ubuntu
To uninstall only the art-nextgen-simulation-tools-profiles package we can use the following command:
sudo apt-get remove art-nextgen-simulation-tools-profiles
Uninstall art-nextgen-simulation-tools-profiles And Its Dependencies
To uninstall art-nextgen-simulation-tools-profiles and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove art-nextgen-simulation-tools-profiles
Remove art-nextgen-simulation-tools-profiles Configurations and Data
To remove art-nextgen-simulation-tools-profiles configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge art-nextgen-simulation-tools-profiles
Remove art-nextgen-simulation-tools-profiles configuration, data, and all of its dependencies
We can use the following command to remove art-nextgen-simulation-tools-profiles configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge art-nextgen-simulation-tools-profiles
Dependencies
art-nextgen-simulation-tools-profiles have the following dependencies:
References
Summary
In this tutorial we learn how to install art-nextgen-simulation-tools-profiles package on Ubuntu using different package management tools: apt, apt-get and aptitude.