maq2sam-short command not found

Introduction

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

maq2sam-short: command not found

or when using sudo you get the following error message

sudo: maq2sam-short: command not found

Solutions to maq2sam-short: command not found

How To Fix maq2sam-short: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu maq2sam-short is provided by samtools package.

samtools is:

Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence Alignment/Map) and CRAM formats, does sorting, merging and indexing, and allows one to retrieve reads in any regions swiftly. It is designed to work on a stream, and is able to open a BAM or CRAM (not SAM) file on a remote FTP or HTTP server.

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

sudo apt-get -y install samtools

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

You can also use apt command to install samtools.

sudo apt -y install samtools

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

sudo aptitude install samtools

Summary

In this tutorial we learn how to fix maq2sam-short command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.