mapsembler2_extend command not found

Introduction

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

mapsembler2_extend: command not found

or when using sudo you get the following error message

sudo: mapsembler2_extend: command not found

Solutions to mapsembler2_extend: command not found

How To Fix mapsembler2_extend: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu mapsembler2_extend is provided by mapsembler2 package.

mapsembler2 is:

Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters).

It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.

Mapsembler2 may be used for (not limited to):

• Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced.
• Checks if a gene (input as starter) has an homolog in a set of reads
• Checks if a known enzyme is present in a metagenomic NGS read set.
• Enrich unmappable reads by extending them, possibly making them mappable
• Checks what happens at the extremities of a contig
• Remove contaminants or symbiont reads from a read set

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

sudo apt-get -y install mapsembler2

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

You can also use apt command to install mapsembler2.

sudo apt -y install mapsembler2

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

sudo aptitude install mapsembler2

Summary

In this tutorial we learn how to fix mapsembler2_extend command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.