How To Install minimap2 on Kali Linux
Introduction
In this tutorial we learn how to install minimap2 on Kali Linux.
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 Kali Linux. 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 updateAfter updating apt database, We can install minimap2 using apt-get by running the following command:
sudo apt-get -y install minimap2Install minimap2 Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install minimap2 using apt by running the following command:
sudo apt -y install minimap2Install minimap2 Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.
sudo aptitude updateAfter updating apt database, We can install minimap2 using aptitude by running the following command:
sudo aptitude -y install minimap2How To Uninstall minimap2 on Kali Linux
To uninstall only the minimap2 package we can use the following command:
sudo apt-get remove minimap2Uninstall minimap2 And Its Dependencies
To uninstall minimap2 and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove minimap2Remove minimap2 Configurations and Data
To remove minimap2 configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge minimap2Remove 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 minimap2Dependencies
minimap2 have the following dependencies:
References
Summary
In this tutorial we learn how to install minimap2 package on Kali Linux using different package management tools: apt, apt-get and aptitude.