How To Install soapsnp on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 494 words
Introduction
In this tutorial we learn how to install soapsnp on Ubuntu.
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 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 soapsnp Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install soapsnp using apt-get by running the following command:
sudo apt-get -y install soapsnp
Install 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 soapsnp
Install soapsnp 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 soapsnp using aptitude by running the following command:
sudo aptitude -y install soapsnp
How To Uninstall soapsnp on Ubuntu
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 Ubuntu, we can use the command below:
sudo apt-get -y autoremove soapsnp
Remove soapsnp Configurations and Data
To remove soapsnp configuration and data from Ubuntu 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 Ubuntu using different package management tools: apt, apt-get and aptitude.