How To Install PyroNoiseM on Kali Linux
In this guide, we’ll discuss How To Install PyroNoiseM on Kali Linux.
Also, we will demonstrate how to uninstall and update
PyroNoiseM
.
One-liner install command
For those in a hurry, here's a one-line installation command:
sudo apt-get update && sudo apt -y install ampliconnoise
But if you are interested in the detailed steps with descriptions, the following information is for you.
What is PyroNoiseM
and what are
the ways to install it?
Short description: removal of noise from 454 sequenced PCR amplicons
Before beginning this tutorial, you will need access to a server or computer running Kali Linux. This guide was written specifically with a server running Kali Linux in mind, although it should also work on older, supported versions of the operating system.
Also, make sure you are running a regular, non-root user with sudo privileges configured on your server. When you have an account available, log in as your non-root user to begin.
There are several ways to install PyroNoiseM on Kali Linux. You can use (links are clickable):
In the following sections, we will describe each method in detail. You can choose one of them or refer to the recommended one.
Install PyroNoiseM using apt-get
First, update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt-get
database,
You can install PyroNoiseM using apt
by running the
following command:
sudo apt -y install ampliconnoise
Install PyroNoiseM using apt
Because PyroNoiseM is available in Kali Linux’s default repositories, it is possible to install it from these repositories using the apt packaging system.
To begin, update apt database with apt
using the following command.
sudo apt update
After updating apt
database,
You can install PyroNoiseM using apt
by running the
following command:
sudo apt -y install ampliconnoise
Install PyroNoiseM 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 Kali Linux. Update apt database with aptitude using the following command.
sudo aptitude update
After updating aptitude
database,
You can install PyroNoiseM by running the following command:
sudo aptitude -y install ampliconnoise
How to upgrade (update) a single package PyroNoiseM using apt-get?
First, you will need to update packages index. Run update
command as
usual:
sudo apt-get update
Next, to upgrade only the PyroNoiseM, e.g. single package, you should use the following format with the apt-get command/apt command:
sudo apt-get --only-upgrade install ampliconnoise
Note that this command will not install any new packages! If you wish to install the
package if it doesn't exist you may leave out --only-upgrade
part.
It's Good to Know:
sudo apt-get install ampliconnoise
This will upgrade the package even if is already installed.
How To Uninstall PyroNoiseM from Kali Linux
To uninstall only the PyroNoiseM
package you can execute
the
following command:
sudo apt-get remove ampliconnoise
Uninstall PyroNoiseM and all its dependencies
To uninstall PyroNoiseM and its dependencies that are no longer needed by Kali Linux, you can use the command below:
sudo apt-get -y autoremove ampliconnoise
Remove PyroNoiseM with all configurations and data
To remove PyroNoiseM configuration and data
from your system you can run the following purge
command:
sudo apt-get -y purge ampliconnoise
Remove PyroNoiseM completely (configurations, data and all of its dependencies)
And lastly, you can run the next command to remove absolutely everything related to PyroNoiseM package, e.g.: configurations, data and all of its dependencies. Just use this command:
sudo apt-get -y autoremove --purge ampliconnoise
Extra info and code examples
AmpliconNoise is a package of applications to clean up high-throughput sequence data. It consists of three main parts: Pyronoise - does flowgram-based clustering to spot misreads SeqNoise - removes PCR point mutations Perseus - removes PCR chimeras without the need for a set of reference sequences Previously there was a standalone "Pyronoise" by the same authors and this package includes an updated version. There is also a "Denoiser" in Qiime which is related but distinct.
- Maintainer: Debian Med Packaging Team
- Sources url: https://github.com/lanzen/ampliconnoise
- Section/Category: science
Conclusion
You now have a full guide on how to install PyroNoiseM
using apt, apt-get and aptitude tools.
Also, we showed how to update as a single package and different ways to uninstall
the PyroNoiseM from Kali Linux.