How To Install samblaster on Kali Linux

Introduction

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

What is samblaster

samblaster is:

Current “next-generation” sequencing technologies cannot tell what exact sequence they will be reading. They take what is available. And if some sequences are read very often, then this needs some extra biomedical thinking. The genome could for instance be duplicated.

samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.

There are three methods to install samblaster 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 samblaster Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install samblaster using apt-get by running the following command:

sudo apt-get -y install samblaster

Install samblaster Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install samblaster using apt by running the following command:

sudo apt -y install samblaster

Install samblaster 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 samblaster using aptitude by running the following command:

sudo aptitude -y install samblaster

How To Uninstall samblaster on Kali Linux

To uninstall only the samblaster package we can use the following command:

sudo apt-get remove samblaster

Uninstall samblaster And Its Dependencies

To uninstall samblaster and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove samblaster

Remove samblaster Configurations and Data

To remove samblaster configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge samblaster

Remove samblaster configuration, data, and all of its dependencies

We can use the following command to remove samblaster configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge samblaster

Dependencies

samblaster have the following dependencies:

• libc6
• libstdc++6

References

• samblaster website

Summary

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