How To Install tophat-recondition on Kali Linux

Introduction

In this tutorial we learn how to install tophat-recondition on Kali Linux.

What is tophat-recondition

tophat-recondition is:

tophat-recondition is a post-processor for TopHat unmapped reads (contained in unmapped.bam), making them compatible with downstream tools (e.g., the Picard suite, samtools, GATK) (TopHat issue #17). It also works around bugs in TopHat:

• the “mate is unmapped” SAM flag is not set on any reads in the unmapped.bam file (TopHat issue #3)
• the mapped mate of an unmapped read can be absent from accepted_hits.bam, creating a mismatch between the file and the unmapped read’s flags (TopHat issue #16)

There are three methods to install tophat-recondition 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 tophat-recondition Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install tophat-recondition using apt-get by running the following command:

sudo apt-get -y install tophat-recondition

Install tophat-recondition Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install tophat-recondition using apt by running the following command:

sudo apt -y install tophat-recondition

Install tophat-recondition 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 tophat-recondition using aptitude by running the following command:

sudo aptitude -y install tophat-recondition

How To Uninstall tophat-recondition on Kali Linux

To uninstall only the tophat-recondition package we can use the following command:

sudo apt-get remove tophat-recondition

Uninstall tophat-recondition And Its Dependencies

To uninstall tophat-recondition and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove tophat-recondition

Remove tophat-recondition Configurations and Data

To remove tophat-recondition configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge tophat-recondition

Remove tophat-recondition configuration, data, and all of its dependencies

We can use the following command to remove tophat-recondition configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge tophat-recondition

Dependencies

tophat-recondition have the following dependencies:

• python3

References

• tophat-recondition website

Summary

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