How To Install snap-aligner on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 424 words
Introduction
In this tutorial we learn how to install snap-aligner on Ubuntu.
What is snap-aligner
snap-aligner is:
SNAP is a new sequence aligner that is 3-20x faster and just as accurate as existing tools like BWA-mem, Bowtie2 and Novoalign. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools (in some cases) and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.
There are three methods to install snap-aligner 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 snap-aligner Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install snap-aligner using apt-get by running the following command:
sudo apt-get -y install snap-aligner
Install snap-aligner Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install snap-aligner using apt by running the following command:
sudo apt -y install snap-aligner
Install snap-aligner 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 snap-aligner using aptitude by running the following command:
sudo aptitude -y install snap-aligner
How To Uninstall snap-aligner on Ubuntu
To uninstall only the snap-aligner package we can use the following command:
sudo apt-get remove snap-aligner
Uninstall snap-aligner And Its Dependencies
To uninstall snap-aligner and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove snap-aligner
Remove snap-aligner Configurations and Data
To remove snap-aligner configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge snap-aligner
Remove snap-aligner configuration, data, and all of its dependencies
We can use the following command to remove snap-aligner configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge snap-aligner
Dependencies
snap-aligner have the following dependencies:
References
Summary
In this tutorial we learn how to install snap-aligner package on Ubuntu using different package management tools: apt, apt-get and aptitude.