How To Install kraken2 on Kali Linux

In this tutorial we learn how to install kraken2 on Kali Linux. kraken2 is taxonomic classification system using exact k-mer matches

Introduction

In this tutorial we learn how to install kraken2 on Kali Linux.

What is kraken2

kraken2 is:

Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. [see: Kraken 1’s Webpage for more details].

Kraken 2 provides significant improvements to Kraken 1, with faster database build times, smaller database sizes, and faster classification speeds. These improvements were achieved by the following updates to the Kraken classification program:

  1. Storage of Minimizers: Instead of storing/querying entire k-mers, Kraken 2 stores minimizers (l-mers) of each k-mer. The length of each l-mer must be ?? the k-mer length. Each k-mer is treated by Kraken 2 as if its LCA is the same as its minimizer’s LCA.
  2. Introduction of Spaced Seeds: Kraken 2 also uses spaced seeds to store and query minimizers to improve classification accuracy.
  3. Database Structure: While Kraken 1 saved an indexed and sorted list of k-mer/LCA pairs, Kraken 2 uses a compact hash table. This hash table is a probabilistic data structure that allows for faster queries and lower memory requirements. However, this data structure does have a <1% chance of returning the incorrect LCA or returning an LCA for a non-inserted minimizer. Users can compensate for this possibility by using Kraken’s confidence scoring thresholds.
  4. Protein Databases: Kraken 2 allows for databases built from amino acid sequences. When queried, Kraken 2 performs a six-frame translated search of the query sequences against the database.
  5. 16S Databases: Kraken 2 also provides support for databases not based on NCBI’s taxonomy. Currently, these include the 16S databases: Greengenes, SILVA, and RDP.

There are three methods to install kraken2 on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install kraken2 Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install kraken2 using apt-get by running the following command:

sudo apt-get -y install kraken2

Install kraken2 Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install kraken2 using apt by running the following command:

sudo apt -y install kraken2

Install kraken2 Using aptitude

If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install kraken2 using aptitude by running the following command:

sudo aptitude -y install kraken2

How To Uninstall kraken2 on Kali Linux

To uninstall only the kraken2 package we can use the following command:

sudo apt-get remove kraken2

Uninstall kraken2 And Its Dependencies

To uninstall kraken2 and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove kraken2

Remove kraken2 Configurations and Data

To remove kraken2 configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge kraken2

Remove kraken2 configuration, data, and all of its dependencies

We can use the following command to remove kraken2 configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge kraken2

Dependencies

kraken2 have the following dependencies:

References

Summary

In this tutorial we learn how to install kraken2 package on Kali Linux using different package management tools: apt, apt-get and aptitude.