How To Install sortmerna on Ubuntu 18.04
Introduction
In this tutorial we learn how to install sortmerna on Ubuntu 18.04.
What is sortmerna
sortmerna is:
SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. Additional applications include OTU-picking and taxonomy assignation available through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1). SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user. Optionally, it can provide high quality local alignments of rRNA reads against the rRNA database. SortMeRNA works with Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.
There are three methods to install sortmerna 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 sortmerna Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install sortmerna using apt-get by running the following command:
sudo apt-get -y install sortmerna
Install sortmerna Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install sortmerna using apt by running the following command:
sudo apt -y install sortmerna
Install sortmerna 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 sortmerna using aptitude by running the following command:
sudo aptitude -y install sortmerna
How To Uninstall sortmerna on Ubuntu 18.04
To uninstall only the sortmerna package we can use the following command:
sudo apt-get remove sortmerna
Uninstall sortmerna And Its Dependencies
To uninstall sortmerna and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove sortmerna
Remove sortmerna Configurations and Data
To remove sortmerna configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge sortmerna
Remove sortmerna configuration, data, and all of its dependencies
We can use the following command to remove sortmerna configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge sortmerna
References
Summary
In this tutorial we learn how to install sortmerna package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
