sambamba command not found

Introduction

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

sambamba: command not found

or when using sudo you get the following error message

sudo: sambamba: command not found

Solutions to sambamba: command not found

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

In Ubuntu sambamba is provided by sambamba package.

sambamba is:

Sambamba positions itself as a performant alternative to samtools and provides tools for

• Powerful filtering with sambamba view –filter
• Picard-like SAM header merging in the merge tool
• Optional for operations on whole BAMs
• Fast copying of a region to a new file with the slice tool
• Duplicate marking/removal, using the Picard criteria

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

sudo apt-get -y install sambamba

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

You can also use apt command to install sambamba.

sudo apt -y install sambamba

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

sudo aptitude install sambamba

Summary

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