How To Install nanopolish on Kali Linux

Introduction

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

What is nanopolish

nanopolish is:

Nanopolish uses a signal-level hidden Markov model for consensus calling of nanopore genome sequencing data. It can perform signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more.

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

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

sudo apt-get update

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

sudo apt-get -y install nanopolish

Install nanopolish Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install nanopolish

Install nanopolish 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 nanopolish using aptitude by running the following command:

sudo aptitude -y install nanopolish

How To Uninstall nanopolish on Kali Linux

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

sudo apt-get remove nanopolish

Uninstall nanopolish And Its Dependencies

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

sudo apt-get -y autoremove nanopolish

Remove nanopolish Configurations and Data

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

sudo apt-get -y purge nanopolish

Remove nanopolish configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge nanopolish

Dependencies

nanopolish have the following dependencies:

• libc6
• libgcc-s1
• libgomp1
• libhdf5-103-1
• libhts3
• libstdc++6
• zlib1g

References

• nanopolish website

Summary

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