How To Install bbmap on Kali Linux

Introduction

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

What is bbmap

bbmap is:

BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels.

BBMap is multithreaded as well as the other tools bundled into this package for instance:

BBNorm: Kmer-based error-correction and normalization tool.

Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity.

Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s.

BBDuk: Filters, trims, or masks reads with kmer matches to an artifact/contaminant file.

There are three methods to install bbmap 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 bbmap Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install bbmap

Install bbmap Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install bbmap

Install bbmap 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 bbmap using aptitude by running the following command:

sudo aptitude -y install bbmap

How To Uninstall bbmap on Kali Linux

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

sudo apt-get remove bbmap

Uninstall bbmap And Its Dependencies

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

sudo apt-get -y autoremove bbmap

Remove bbmap Configurations and Data

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

sudo apt-get -y purge bbmap

Remove bbmap configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge bbmap

Dependencies

bbmap have the following dependencies:

• libmpj-java

References

• bbmap website

Summary

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