How To Install e-mem on Kali Linux

In this tutorial we learn how to install e-mem on Kali Linux. e-mem is Efficient computation of Maximal Exact Matches for very large genomes

Introduction

In this tutorial we learn how to install e-mem on Kali Linux.

What is e-mem

e-mem is:

E-MEM enables efficient computation of Maximal Exact Matches (MEMs) that does not use full text indexes. The algorithm uses much less space and is highly amenable to parallelization. It can compute all MEMs of minimum length 100 between the whole human and mouse genomes on a 12 core machine in 10 min and 2 GB of memory; the required memory can be as low as 600 MB. It can run efficiently genomes of any size. Extensive testing and comparison with currently best algorithms is provided.

Mummer has many different scripts where one of the key program is MEM computation. In all the scripts, the MEM computation program can be replaced with e-mem with ease for better performance.

There are three methods to install e-mem 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 e-mem Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install e-mem

Install e-mem Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install e-mem

Install e-mem 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 e-mem using aptitude by running the following command:

sudo aptitude -y install e-mem

How To Uninstall e-mem on Kali Linux

To uninstall only the e-mem package we can use the following command:

sudo apt-get remove e-mem

Uninstall e-mem And Its Dependencies

To uninstall e-mem and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove e-mem

Remove e-mem Configurations and Data

To remove e-mem configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge e-mem

Remove e-mem configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge e-mem

Dependencies

e-mem have the following dependencies:

References

Summary

In this tutorial we learn how to install e-mem package on Kali Linux using different package management tools: apt, apt-get and aptitude.