Introduction
In this tutorial we learn how to install kmc on Ubuntu 22.04.
What is kmc
kmc is:
The kmc software is designed for counting k-mers (sequences of
consecutive k symbols) in a set of reads. K-mer counting is
important for many bioinformatics applications, e.g. developing de Bruijn
graph assemblers.
Building de Bruijn graphs is a commonly used approach for genome
assembly with data from second-generation sequencing.
Unfortunately, sequencing errors (frequent in practice)
result in huge memory requirements for de Bruijn graphs, as well
as long build time. One of the popular approaches to handle this
problem is filtering the input reads in such a way that unique k-mers
(very likely obtained as a result of an error) are discarded.
Thus, KMC scans the raw reads and produces a compact representation
of all non-unique reads accompanied with number of their occurrences.
The algorithm implemented in KMC makes use mostly of disk space rather
than RAM, which allows one to use KMC even on rather typical personal
computers. When run on high-end servers (what is necessary for KMC
competitors) it outperforms them in both memory requirements and
speed of computation. The disk space necessary for computation is in
order of the size of input data (usually it is smaller).
There are three methods to install kmc 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 kmc Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install kmc using apt-get by running the following command:
sudo apt-get -y install kmc
Install kmc Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install kmc using apt by running the following command:
sudo apt -y install kmc
Install kmc 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 kmc using aptitude by running the following command:
sudo aptitude -y install kmc
How To Uninstall kmc on Ubuntu 22.04
To uninstall only the kmc package we can use the following command:
sudo apt-get remove kmc
Uninstall kmc And Its Dependencies
To uninstall kmc and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove kmc
Remove kmc Configurations and Data
To remove kmc configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge kmc
Remove kmc configuration, data, and all of its dependencies
We can use the following command to remove kmc configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge kmc
References
Summary
In this tutorial we learn how to install kmc package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
