How To Install samclip on Kali Linux

Introduction

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

What is samclip

samclip is:

Most short read aligners perform local alignment of reads to the reference genome. Examples includes bwa mem, minimap2, and bowtie2 (unless in –end-to-end mode). This means the ends of the read may not be part of the best alignment.

This can be caused by:

• adapter sequences (aren’t in the reference)
• poor quality bases (mismatches only make the alignment score worse)
• structural variation in your sample compared to the reference
• reads overlapping the start and end of contigs (including circular genomes)

Read aligners output a SAM file. Column 6 in this format stores the CIGAR string. which describes which parts of the read aligned and which didn’t. The unaligned ends of the read can be “soft” or “hard” clipped, denoted with S and H at each end of the CIGAR string. It is possible for both types to be present, but that is not common. Soft and hard don’t mean anything biologically, they just refer to whether the full read sequence is in the SAM file or not.

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

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

sudo apt-get update

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

sudo apt-get -y install samclip

Install samclip Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install samclip

Install samclip 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 samclip using aptitude by running the following command:

sudo aptitude -y install samclip

How To Uninstall samclip on Kali Linux

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

sudo apt-get remove samclip

Uninstall samclip And Its Dependencies

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

sudo apt-get -y autoremove samclip

Remove samclip Configurations and Data

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

sudo apt-get -y purge samclip

Remove samclip configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge samclip

Dependencies

samclip have the following dependencies:

• perl

References

• samclip website

Summary

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