How To Install reapr on Kali Linux

In this tutorial we learn how to install reapr on Kali Linux. reapr is universal tool for genome assembly evaluation

Introduction

In this tutorial we learn how to install reapr on Kali Linux.

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 Kali Linux. 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 on Kali Linux 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 apt database, We can install reapr using aptitude by running the following command:

sudo aptitude -y install reapr

How To Uninstall reapr on Kali Linux

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 Kali Linux, we can use the command below:

sudo apt-get -y autoremove reapr

Remove reapr Configurations and Data

To remove reapr configuration and data from Kali Linux 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

Dependencies

reapr have the following dependencies:

References

Summary

In this tutorial we learn how to install reapr package on Kali Linux using different package management tools: apt, apt-get and aptitude.