kraken-build command not found

Introduction

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

kraken-build: command not found

or when using sudo you get the following error message

sudo: kraken-build: command not found

Solutions to kraken-build: command not found

How To Fix kraken-build: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu kraken-build is provided by kraken package.

kraken is:

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.

In its fastest mode of operation, for a simulated metagenome of 100 bp reads, Kraken processed over 4 million reads per minute on a single core, over 900 times faster than Megablast and over 11 times faster than the abundance estimation program MetaPhlAn. Kraken’s accuracy is comparable with Megablast, with slightly lower sensitivity and very high precision.

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

sudo apt-get -y install kraken

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

You can also use apt command to install kraken.

sudo apt -y install kraken

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

sudo aptitude install kraken

Summary

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