ngmlr command not found

Introduction

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

ngmlr: command not found

or when using sudo you get the following error message

sudo: ngmlr: command not found

Solutions to ngmlr: command not found

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

In Ubuntu ngmlr is provided by ngmlr package.

ngmlr is:

Ngmlr is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith- Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments.

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

sudo apt-get -y install ngmlr

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

You can also use apt command to install ngmlr.

sudo apt -y install ngmlr

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

sudo aptitude install ngmlr

Summary

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