SNAPCommand command not found

Introduction

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

SNAPCommand: command not found

or when using sudo you get the following error message

sudo: SNAPCommand: command not found

Solutions to SNAPCommand: command not found

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

In Ubuntu SNAPCommand is provided by snap-aligner package.

snap-aligner is:

SNAP is a new sequence aligner that is 3-20x faster and just as accurate as existing tools like BWA-mem, Bowtie2 and Novoalign. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools (in some cases) and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.

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

sudo apt-get -y install snap-aligner

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

You can also use apt command to install snap-aligner.

sudo apt -y install snap-aligner

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

sudo aptitude install snap-aligner

Summary

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