How To Install samblaster on Ubuntu 20.04
Introduction
In this tutorial we learn how to install samblaster
on Ubuntu 20.04.
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 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 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 20.04
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 20.04, 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 20.04 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
References
Summary
In this tutorial we learn how to install samblaster
package on Ubuntu 20.04 using different package management tools: apt
, apt-get
and aptitude
.