How To Install samblaster on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 419 words
Introduction
In this tutorial we learn how to install samblaster on Ubuntu.
What is samblaster
samblaster is:
Current “next-generation” sequencing technologies cannot tell what exact sequence they will be reading. They take what is available. And if some sequences are read very often, then this needs some extra biomedical thinking. The genome could for instance be duplicated.
samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
There are three methods to install samblaster on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install samblaster Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install samblaster using apt-get by running the following command:
sudo apt-get -y install samblaster
Install samblaster Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install samblaster using apt by running the following command:
sudo apt -y install samblaster
Install samblaster 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 samblaster using aptitude by running the following command:
sudo aptitude -y install samblaster
How To Uninstall samblaster on Ubuntu
To uninstall only the samblaster package we can use the following command:
sudo apt-get remove samblaster
Uninstall samblaster And Its Dependencies
To uninstall samblaster and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove samblaster
Remove samblaster Configurations and Data
To remove samblaster configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge samblaster
Remove samblaster configuration, data, and all of its dependencies
We can use the following command to remove samblaster configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge samblaster
Dependencies
samblaster have the following dependencies:
References
Summary
In this tutorial we learn how to install samblaster package on Ubuntu using different package management tools: apt, apt-get and aptitude.