How To Install mash on Kali Linux

In this tutorial we learn how to install mash on Kali Linux. mash is fast genome and metagenome distance estimation using MinHash

Introduction

In this tutorial we learn how to install mash on Kali Linux.

What is mash

mash is:

Mash uses MinHash locality-sensitive hashing to reduce large biosequences to a representative sketch and rapidly estimate pairwise distances between genomes or metagenomes. Mash sketch databases effectively delineate known species boundaries, allow construction of approximate phylogenies, and can be searched in seconds using assembled genomes or raw sequencing runs from Illumina, Pacific Biosciences, and Oxford Nanopore. For metagenomics, Mash scales to thousands of samples and can replicate Human Microbiome Project and Global Ocean Survey results in a fraction of the time.

There are three methods to install mash 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 mash Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install mash

Install mash Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install mash

Install mash 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 mash using aptitude by running the following command:

sudo aptitude -y install mash

How To Uninstall mash on Kali Linux

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

sudo apt-get remove mash

Uninstall mash And Its Dependencies

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

sudo apt-get -y autoremove mash

Remove mash Configurations and Data

To remove mash configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge mash

Remove mash configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge mash

Dependencies

mash have the following dependencies:

References

Summary

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