How To Install reapr on Ubuntu 18.04
Introduction
In this tutorial we learn how to install reapr on Ubuntu 18.04.
What is reapr
reapr is:
REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.
The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly.
There are three methods to install reapr on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install reapr Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install reapr using apt-get by running the following command:
sudo apt-get -y install reapr
Install reapr Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install reapr using apt by running the following command:
sudo apt -y install reapr
Install reapr 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 reapr using aptitude by running the following command:
sudo aptitude -y install reapr
How To Uninstall reapr on Ubuntu 18.04
To uninstall only the reapr package we can use the following command:
sudo apt-get remove reapr
Uninstall reapr And Its Dependencies
To uninstall reapr and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove reapr
Remove reapr Configurations and Data
To remove reapr configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge reapr
Remove reapr configuration, data, and all of its dependencies
We can use the following command to remove reapr configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge reapr
References
Summary
In this tutorial we learn how to install reapr package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
