MindTheGap command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

MindTheGap: command not found

or when using sudo you get the following error message

sudo: MindTheGap: command not found

Solutions to MindTheGap: command not found

How To Fix MindTheGap: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu MindTheGap is provided by mindthegap package.

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.

To fix this problem, we can install more using the command below.

sudo apt-get -y install mindthegap

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install mindthegap.

sudo apt -y install mindthegap

Or if you have aptitude installed you can use the following command.

sudo aptitude install mindthegap

Summary

In this tutorial we learn how to fix MindTheGap command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.