How To Install mash on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 410 words
Introduction
In this tutorial we learn how to install mash on Ubuntu.
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. 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
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, 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 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 Ubuntu using different package management tools: apt, apt-get and aptitude.