bowtie2sam.pl command not found

Introduction

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

bowtie2sam.pl: command not found

or when using sudo you get the following error message

sudo: bowtie2sam.pl: command not found

Solutions to bowtie2sam.pl: command not found

How To Fix bowtie2sam.pl: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu bowtie2sam.pl 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 bowtie2sam.pl command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.