How To Install kallisto on Kali Linux

In this tutorial we learn how to install kallisto on Kali Linux. kallisto is near-optimal RNA-Seq quantification

Introduction

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

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 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 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 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 kallisto using aptitude by running the following command:

sudo aptitude -y install kallisto

How To Uninstall kallisto on Kali Linux

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 Kali Linux, we can use the command below:

sudo apt-get -y autoremove kallisto

Remove kallisto Configurations and Data

To remove kallisto configuration and data from Kali Linux 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

Dependencies

kallisto have the following dependencies:

References

Summary

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