How To Install nanopolish on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 382 words
Introduction
In this tutorial we learn how to install nanopolish on Ubuntu.
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 Ubuntu. 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 first since aptitude is usually not installed by default on Ubuntu. 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 Ubuntu
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 Ubuntu, we can use the command below:
sudo apt-get -y autoremove nanopolish
Remove nanopolish Configurations and Data
To remove nanopolish configuration and data from Ubuntu 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:
References
Summary
In this tutorial we learn how to install nanopolish package on Ubuntu using different package management tools: apt, apt-get and aptitude.