How To Install mindthegap on Kali Linux

Introduction

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

What is mindthegap

mindthegap is:

Designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. It takes as input a set of reads and a reference genome. It outputs two sets of FASTA sequences: one is the set of breakpoints of detection insertion sites, the other is the set of assembled insertions for each breakpoint. MindTheGap can also be used as a genome assembly finishing tool. It can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. It outputs the results in gfa file.

There are three methods to install mindthegap 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 mindthegap Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install mindthegap

Install mindthegap Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install mindthegap using apt by running the following command:

sudo apt -y install mindthegap

Install mindthegap 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 mindthegap using aptitude by running the following command:

sudo aptitude -y install mindthegap

How To Uninstall mindthegap on Kali Linux

To uninstall only the mindthegap package we can use the following command:

sudo apt-get remove mindthegap

Uninstall mindthegap And Its Dependencies

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

sudo apt-get -y autoremove mindthegap

Remove mindthegap Configurations and Data

To remove mindthegap configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge mindthegap

Remove mindthegap configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge mindthegap

Dependencies

mindthegap have the following dependencies:

• libc6
• libgatbcore3
• libgcc-s1
• libhdf5-103-1
• libstdc++6

References

• mindthegap website

Summary

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