How To Install kallisto on Ubuntu 22.04
Introduction
In this tutorial we learn how to install kallisto on Ubuntu 22.04.
What is kallisto
kallisto is:
Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate than existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools.
There are three methods to install kallisto 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 kallisto Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install kallisto using apt-get by running the following command:
sudo apt-get -y install kallisto
Install kallisto Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install kallisto using apt by running the following command:
sudo apt -y install kallisto
Install kallisto 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 kallisto using aptitude by running the following command:
sudo aptitude -y install kallisto
How To Uninstall kallisto on Ubuntu 22.04
To uninstall only the kallisto package we can use the following command:
sudo apt-get remove kallisto
Uninstall kallisto And Its Dependencies
To uninstall kallisto and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove kallisto
Remove kallisto Configurations and Data
To remove kallisto configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge kallisto
Remove kallisto configuration, data, and all of its dependencies
We can use the following command to remove kallisto configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge kallisto
References
Summary
In this tutorial we learn how to install kallisto package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
