How To Install snap-aligner on Kali Linux

In this tutorial we learn how to install snap-aligner on Kali Linux. snap-aligner is Scalable Nucleotide Alignment Program

Introduction

In this tutorial we learn how to install snap-aligner on Kali Linux.

What is snap-aligner

snap-aligner is:

SNAP is a new sequence aligner that is 3-20x faster and just as accurate as existing tools like BWA-mem, Bowtie2 and Novoalign. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools (in some cases) and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.

There are three methods to install snap-aligner 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 snap-aligner Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install snap-aligner

Install snap-aligner Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install snap-aligner

Install snap-aligner 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 snap-aligner using aptitude by running the following command:

sudo aptitude -y install snap-aligner

How To Uninstall snap-aligner on Kali Linux

To uninstall only the snap-aligner package we can use the following command:

sudo apt-get remove snap-aligner

Uninstall snap-aligner And Its Dependencies

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

sudo apt-get -y autoremove snap-aligner

Remove snap-aligner Configurations and Data

To remove snap-aligner configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge snap-aligner

Remove snap-aligner configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge snap-aligner

Dependencies

snap-aligner have the following dependencies:

References

Summary

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