How To Install q2-dada2 on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 509 words
Introduction
In this tutorial we learn how to install q2-dada2 on Ubuntu.
What is q2-dada2
q2-dada2 is:
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line, graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed.
This package wraps the dada2 R package in BioConductor for modeling and correcting Illumina-sequenced amplicon errors. This was shown to improve the sensitivity of diversity analyses.
There are three methods to install q2-dada2 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 q2-dada2 Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install q2-dada2 using apt-get by running the following command:
sudo apt-get -y install q2-dada2
Install q2-dada2 Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install q2-dada2 using apt by running the following command:
sudo apt -y install q2-dada2
Install q2-dada2 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 q2-dada2 using aptitude by running the following command:
sudo aptitude -y install q2-dada2
How To Uninstall q2-dada2 on Ubuntu
To uninstall only the q2-dada2 package we can use the following command:
sudo apt-get remove q2-dada2
Uninstall q2-dada2 And Its Dependencies
To uninstall q2-dada2 and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove q2-dada2
Remove q2-dada2 Configurations and Data
To remove q2-dada2 configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge q2-dada2
Remove q2-dada2 configuration, data, and all of its dependencies
We can use the following command to remove q2-dada2 configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge q2-dada2
Dependencies
q2-dada2 have the following dependencies:
References
Summary
In this tutorial we learn how to install q2-dada2 package on Ubuntu using different package management tools: apt, apt-get and aptitude.