reapr command not found

Introduction

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

reapr: command not found

or when using sudo you get the following error message

sudo: reapr: command not found

Solutions to reapr: command not found

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

In Ubuntu reapr is provided by reapr package.

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.

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

sudo apt-get -y install reapr

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

You can also use apt command to install reapr.

sudo apt -y install reapr

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

sudo aptitude install reapr

Summary

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