How To Install pirs on Debian 9

In this tutorial we learn how to install pirs on Debian 9. pirs is Profile based Illumina pair-end Reads Simulator

Introduction

In this tutorial we learn how to install pirs on Debian 9.

What is pirs

pirs is:

The program pIRS can be used for simulating Illumina PE reads, with a series of characters generated by Illumina sequencing platform, such as insert size distribution, sequencing error(substitution, insertion, deletion), quality score and GC content-coverage bias.

The insert size follows a normal distribution, so users should set the mean value and standard deviation. Usually the standard deviation is set as 1/20 of the mean value. The normal distribution by Box-Muller method is simulated.

The program simulates sequencing error, quality score and GC content- coverage bias according to the empirical distribution profile. Some default profiles counted from lots of real sequencing data are provided.

To simulate reads from diploid genome, users should simulate the diploid genome sequence firstly by setting the ratio of heterozygosis SNP, heterozygosis InDel and structure variation.

There are three methods to install pirs on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install pirs Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install pirs using apt-get by running the following command:

sudo apt-get -y install pirs

Install pirs Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install pirs using apt by running the following command:

sudo apt -y install pirs

Install pirs 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 Debian. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install pirs using aptitude by running the following command:

sudo aptitude -y install pirs

How To Uninstall pirs on Debian 9

To uninstall only the pirs package we can use the following command:

sudo apt-get remove pirs

Uninstall pirs And Its Dependencies

To uninstall pirs and its dependencies that are no longer needed by Debian 9, we can use the command below:

sudo apt-get -y autoremove pirs

Remove pirs Configurations and Data

To remove pirs configuration and data from Debian 9 we can use the following command:

sudo apt-get -y purge pirs

Remove pirs configuration, data, and all of its dependencies

We can use the following command to remove pirs configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge pirs

Dependencies

pirs have the following dependencies:

References

Summary

In this tutorial we learn how to install pirs package on Debian 9 using different package management tools: apt, apt-get and aptitude.