How To Install mapsembler2 on Ubuntu 22.04
Introduction
In this tutorial we learn how to install mapsembler2 on Ubuntu 22.04.
What is mapsembler2
mapsembler2 is:
Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters).
It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
Mapsembler2 may be used for (not limited to):
- Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced.
- Checks if a gene (input as starter) has an homolog in a set of reads
- Checks if a known enzyme is present in a metagenomic NGS read set.
- Enrich unmappable reads by extending them, possibly making them mappable
- Checks what happens at the extremities of a contig
- Remove contaminants or symbiont reads from a read set
There are three methods to install mapsembler2 on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install mapsembler2 Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install mapsembler2 using apt-get by running the following command:
sudo apt-get -y install mapsembler2
Install mapsembler2 Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install mapsembler2 using apt by running the following command:
sudo apt -y install mapsembler2
Install mapsembler2 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 mapsembler2 using aptitude by running the following command:
sudo aptitude -y install mapsembler2
How To Uninstall mapsembler2 on Ubuntu 22.04
To uninstall only the mapsembler2 package we can use the following command:
sudo apt-get remove mapsembler2
Uninstall mapsembler2 And Its Dependencies
To uninstall mapsembler2 and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove mapsembler2
Remove mapsembler2 Configurations and Data
To remove mapsembler2 configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge mapsembler2
Remove mapsembler2 configuration, data, and all of its dependencies
We can use the following command to remove mapsembler2 configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge mapsembler2
References
Summary
In this tutorial we learn how to install mapsembler2 package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
