How To Install mash on Ubuntu 22.04
Introduction
In this tutorial we learn how to install mash
on Ubuntu 22.04.
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 Ubuntu 22.04. 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 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 mash
using aptitude
by running the following command:
sudo aptitude -y install mash
How To Uninstall mash on Ubuntu 22.04
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 Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove mash
Remove mash Configurations and Data
To remove mash
configuration and data from Ubuntu 22.04 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
References
Summary
In this tutorial we learn how to install mash
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.