samblaster command not found

Introduction

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

samblaster: command not found

or when using sudo you get the following error message

sudo: samblaster: command not found

Solutions to samblaster: command not found

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

In Ubuntu samblaster is provided by samblaster package.

samblaster is:

Current “next-generation” sequencing technologies cannot tell what exact sequence they will be reading. They take what is available. And if some sequences are read very often, then this needs some extra biomedical thinking. The genome could for instance be duplicated.

samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.

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

sudo apt-get -y install samblaster

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

You can also use apt command to install samblaster.

sudo apt -y install samblaster

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

sudo aptitude install samblaster

Summary

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