How To Install minimap2 on Debian 11
Introduction
In this tutorial we learn how to install minimap2 on Debian 11.
What is minimap2
minimap2 is:
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2) finding overlaps between long reads with error rate up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome; (4) aligning Illumina single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full- genome alignment between two closely related species with divergence below ~15%.
For ~10kb noisy reads sequences, minimap2 is tens of times faster than mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more accurate on simulated long reads and produces biologically meaningful alignment ready for downstream analyses. For >100bp Illumina short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data. Detailed evaluations are available from the minimap2 paper or the preprint.
There are three methods to install minimap2 on Debian 11. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install minimap2 Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install minimap2 using apt-get by running the following command:
sudo apt-get -y install minimap2
Install minimap2 Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install minimap2 using apt by running the following command:
sudo apt -y install minimap2
Install minimap2 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 minimap2 using aptitude by running the following command:
sudo aptitude -y install minimap2
How To Uninstall minimap2 on Debian 11
To uninstall only the minimap2 package we can use the following command:
sudo apt-get remove minimap2
Uninstall minimap2 And Its Dependencies
To uninstall minimap2 and its dependencies that are no longer needed by Debian 11, we can use the command below:
sudo apt-get -y autoremove minimap2
Remove minimap2 Configurations and Data
To remove minimap2 configuration and data from Debian 11 we can use the following command:
sudo apt-get -y purge minimap2
Remove minimap2 configuration, data, and all of its dependencies
We can use the following command to remove minimap2 configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge minimap2
Dependencies
minimap2 have the following dependencies:
References
Summary
In this tutorial we learn how to install minimap2 package on Debian 11 using different package management tools: apt, apt-get and aptitude.