How To Install qiime on Ubuntu 18.04
Introduction
In this tutorial we learn how to install qiime on Ubuntu 18.04.
What is qiime
qiime is:
QIIME (canonically pronounced ‘Chime’) is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field. A standard QIIME analysis begins with sequence data from one or more sequencing platforms, including
- Sanger,
- Roche/454, and
- Illumina GAIIx. With all the underlying tools installed, of which not all are yet available in Debian (or any other Linux distribution), QIIME can perform
- library de-multiplexing and quality filtering;
- denoising with PyroNoise;
- OTU and representative set picking with uclust, cdhit, mothur, BLAST, or other tools;
- taxonomy assignment with BLAST or the RDP classifier;
- sequence alignment with PyNAST, muscle, infernal, or other tools;
- phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;
- alpha diversity and rarefaction, including visualization of results, using over 20 metrics including Phylogenetic Diversity, chao1, and observed species;
- beta diversity and rarefaction, including visualization of results, using over 25 metrics including weighted and unweighted UniFrac, Euclidean distance, and Bray-Curtis;
- summarization and visualization of taxonomic composition of samples using pie charts and histograms and many other features.
QIIME includes parallelization capabilities for many of the computationally intensive steps. By default, these are configured to utilize a mutli-core environment, and are easily configured to run in a cluster environment. QIIME is built in Python using the open-source PyCogent toolkit. It makes extensive use of unit tests, and is highly modular to facilitate custom analyses.
There are three methods to install qiime on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install qiime Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install qiime using apt-get by running the following command:
sudo apt-get -y install qiime
Install qiime Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install qiime using apt by running the following command:
sudo apt -y install qiime
Install qiime 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 qiime using aptitude by running the following command:
sudo aptitude -y install qiime
How To Uninstall qiime on Ubuntu 18.04
To uninstall only the qiime package we can use the following command:
sudo apt-get remove qiime
Uninstall qiime And Its Dependencies
To uninstall qiime and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove qiime
Remove qiime Configurations and Data
To remove qiime configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge qiime
Remove qiime configuration, data, and all of its dependencies
We can use the following command to remove qiime configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge qiime
References
Summary
In this tutorial we learn how to install qiime package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
