Introduction
In this tutorial we learn how to install soapaligner on Kali Linux.
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 Kali Linux. 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 updateAfter 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 soapalignerInstall soapaligner Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. 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 Kali Linux
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 Kali Linux, we can use the command below:
sudo apt-get -y autoremove soapaligner
Remove soapaligner Configurations and Data
To remove soapaligner configuration and data from Kali Linux 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 Kali Linux using different package management tools: apt, apt-get and aptitude.
