bowtie2 command not found

Introduction

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

bowtie2: command not found

or when using sudo you get the following error message

sudo: bowtie2: command not found

Solutions to bowtie2: command not found

How To Fix bowtie2: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu bowtie2 is provided by bowtie2 package.

bowtie2 is:

is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.

Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes

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

sudo apt-get -y install bowtie2

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

You can also use apt command to install bowtie2.

sudo apt -y install bowtie2

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

sudo aptitude install bowtie2

Summary

In this tutorial we learn how to fix bowtie2 command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.