Introduction
In this tutorial we learn how to install soapsnp on Kali Linux.
What is soapsnp
soapsnp is:
For getting ideas on the cause of diseases or their response to
therapy, and for understanding either for a particular patient,
doctors around the globe are starting to look at the genes or the
whole genome and how that sequence is different from a healthy /
well responding individual.
SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis
Package). The program is a resequencing utility. It assembles the
consensus sequence for the genome of a newly sequenced individual based
on the alignment of the raw sequencing reads on a known reference. SNPs
can then be identified on the consensus sequence through the comparison
with the reference.
SOAPsnp uses a method based on Bayes’ theorem (the reverse probability
model) to call consensus genotype by carefully considering the data
quality, alignment, and recurring experimental errors. All these kinds
of information was integrated into a single quality score for each base
in PHRED scale to measure the accuracy of consensus calling. Currently,
it supports the alignment format of SOAPaligner (soap2).
There are three methods to install soapsnp 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 soapsnp Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install soapsnp using apt-get by running the following command:
sudo apt-get -y install soapsnpInstall soapsnp Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install soapsnp using apt by running the following command:
sudo apt -y install soapsnpInstall soapsnp 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 updateAfter updating apt database, We can install soapsnp using aptitude by running the following command:
sudo aptitude -y install soapsnp
How To Uninstall soapsnp on Kali Linux
To uninstall only the soapsnp package we can use the following command:
sudo apt-get remove soapsnp
Uninstall soapsnp And Its Dependencies
To uninstall soapsnp and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove soapsnp
Remove soapsnp Configurations and Data
To remove soapsnp configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge soapsnp
Remove soapsnp configuration, data, and all of its dependencies
We can use the following command to remove soapsnp configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge soapsnp
Dependencies
soapsnp have the following dependencies:
References
Summary
In this tutorial we learn how to install soapsnp package on Kali Linux using different package management tools: apt, apt-get and aptitude.
