How To Install porechop on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 402 words
Introduction
In this tutorial we learn how to install porechop on Ubuntu.
What is porechop
porechop is:
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity. Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.
There are three methods to install porechop 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 porechop Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install porechop using apt-get by running the following command:
sudo apt-get -y install porechop
Install porechop Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install porechop using apt by running the following command:
sudo apt -y install porechop
Install porechop 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 porechop using aptitude by running the following command:
sudo aptitude -y install porechop
How To Uninstall porechop on Ubuntu
To uninstall only the porechop package we can use the following command:
sudo apt-get remove porechop
Uninstall porechop And Its Dependencies
To uninstall porechop and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove porechop
Remove porechop Configurations and Data
To remove porechop configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge porechop
Remove porechop configuration, data, and all of its dependencies
We can use the following command to remove porechop configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge porechop
Dependencies
porechop have the following dependencies:
References
Summary
In this tutorial we learn how to install porechop package on Ubuntu using different package management tools: apt, apt-get and aptitude.