Introduction
In this tutorial we learn how to install bbmap on Ubuntu 20.04.
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 Ubuntu 20.04. 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 Ubuntu. 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 Ubuntu 20.04
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 Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove bbmap
Remove bbmap Configurations and Data
To remove bbmap configuration and data from Ubuntu 20.04 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
References
Summary
In this tutorial we learn how to install bbmap package on Ubuntu 20.04 using different package management tools: apt, apt-get and aptitude.
