How To Install ngmlr on Kali Linux

In this tutorial we learn how to install ngmlr on Kali Linux. ngmlr is CoNvex Gap-cost alignMents for Long Reads

Introduction

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

What is ngmlr

ngmlr is:

Ngmlr is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith- Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments.

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

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

sudo apt-get update

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

sudo apt-get -y install ngmlr

Install ngmlr Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install ngmlr

Install ngmlr 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 ngmlr using aptitude by running the following command:

sudo aptitude -y install ngmlr

How To Uninstall ngmlr on Kali Linux

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

sudo apt-get remove ngmlr

Uninstall ngmlr And Its Dependencies

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

sudo apt-get -y autoremove ngmlr

Remove ngmlr Configurations and Data

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

sudo apt-get -y purge ngmlr

Remove ngmlr configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge ngmlr

Dependencies

ngmlr have the following dependencies:

References

Summary

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