How To Install soapaligner on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 504 words
Introduction
In this tutorial we learn how to install soapaligner on Ubuntu.
What is soapaligner
soapaligner is:
This package addresses a common problem in bioinformatics that has become routine now also in clinical research: the assembly and comparison of the very long genomic DNA sequences from many short reads that the machines provide.
SOAPaligner/soap2 is a member of the Short Oligonucleotide Analysis Package (SOAP) and an updated version of SOAP software for short oligonucleotide alignment (soap v1). The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length.
SOAPaligner/soap2 benefitted in time and space efficiency by a revolution in the basic data structures and algorithms used. The core algorithms and the indexing data structures (2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).
There are three methods to install soapaligner 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 soapaligner Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install soapaligner using apt-get by running the following command:
sudo apt-get -y install soapaligner
Install soapaligner Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install soapaligner using apt by running the following command:
sudo apt -y install soapaligner
Install soapaligner 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 soapaligner using aptitude by running the following command:
sudo aptitude -y install soapaligner
How To Uninstall soapaligner on Ubuntu
To uninstall only the soapaligner package we can use the following command:
sudo apt-get remove soapaligner
Uninstall soapaligner And Its Dependencies
To uninstall soapaligner and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove soapaligner
Remove soapaligner Configurations and Data
To remove soapaligner configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge soapaligner
Remove soapaligner configuration, data, and all of its dependencies
We can use the following command to remove soapaligner configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge soapaligner
Dependencies
soapaligner have the following dependencies:
References
Summary
In this tutorial we learn how to install soapaligner package on Ubuntu using different package management tools: apt, apt-get and aptitude.