How To Install skewer on Kali Linux

In this tutorial we learn how to install skewer on Kali Linux. skewer is post-processing of high-throughput DNA sequence reads

Introduction

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

What is skewer

skewer is:

skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.

Features

  • Detection and removal of adapter sequences
  • Insertion and deletion allowed in pattern matching
  • Targeted at Single End, Paired End (PE), and Long Mate Pair (LMP) reads
  • Demultiplexing of barcoded sequencing runs
  • Multi-threading support
  • Trimming based on phred quality scores
  • IUPAC characters for barcodes and adapters
  • Compressed input and output support

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

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

sudo apt-get update

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

sudo apt-get -y install skewer

Install skewer Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install skewer

Install skewer 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 skewer using aptitude by running the following command:

sudo aptitude -y install skewer

How To Uninstall skewer on Kali Linux

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

sudo apt-get remove skewer

Uninstall skewer And Its Dependencies

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

sudo apt-get -y autoremove skewer

Remove skewer Configurations and Data

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

sudo apt-get -y purge skewer

Remove skewer configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge skewer

Dependencies

skewer have the following dependencies:

References

Summary

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