ragout-overlap command not found

Introduction

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

ragout-overlap: command not found

or when using sudo you get the following error message

sudo: ragout-overlap: command not found

Solutions to ragout-overlap: command not found

How To Fix ragout-overlap: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu ragout-overlap is provided by ragout package.

ragout is:

Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome-level scaffolding using multiple references. Given initial assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds).

The approach is based on the analysis of genome rearrangements (like inversions or chromosomal translocations) between the input genomes and reconstructing the most parsimonious structure of the target genome.

Ragout now supports both small and large genomes (of mammalian scale and complexity). The assembly of highly polymorphic genomes is currently limited.

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

sudo apt-get -y install ragout

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

You can also use apt command to install ragout.

sudo apt -y install ragout

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

sudo aptitude install ragout

Summary

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