How To Install bbmap on Debian 12
Introduction
In this tutorial we learn how to install bbmap on Debian 12.
What is bbmap
bbmap is:
The BBTools are a collection of small programs to solve recurrent tasks for the creative handling of short biological RNA/DNA sequences. This suite may be best known for its mapper, which is also the name of the project on sourceforge, but several tools have been added over time. All tools are multi-threaded, implemented platform-independently in Java:
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.
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 Debian 12. 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 first since aptitude is usually not installed by default on Debian. 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 Debian 12
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 Debian 12, we can use the command below:
sudo apt-get -y autoremove bbmap
Remove bbmap Configurations and Data
To remove bbmap configuration and data from Debian 12 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:
References
Summary
In this tutorial we learn how to install bbmap package on Debian 12 using different package management tools: apt, apt-get and aptitude.