How To Install smalt on Kali Linux
Introduction
In this tutorial we learn how to install smalt on Kali Linux.
What is smalt
smalt is:
SMALT efficiently aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads.
The software employs a perfect hash index of short words (< 20 nucleotides long), sampled at equidistant steps along the genomic reference sequences.
For each read, potentially matching segments in the reference are identified from seed matches in the index and subsequently aligned with the read using a banded Smith-Waterman algorithm.
The best gapped alignments of each read is reported including a score for the reliability of the best mapping. The user can adjust the trade-off between sensitivity and speed by tuning the length and spacing of the hashed words.
A mode for the detection of split (chimeric) reads is provided. Multi-threaded program execution is supported.
There are three methods to install smalt 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 smalt Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install smalt using apt-get by running the following command:
sudo apt-get -y install smaltInstall smalt Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install smalt using apt by running the following command:
sudo apt -y install smaltInstall smalt 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 smalt using aptitude by running the following command:
sudo aptitude -y install smaltHow To Uninstall smalt on Kali Linux
To uninstall only the smalt package we can use the following command:
sudo apt-get remove smaltUninstall smalt And Its Dependencies
To uninstall smalt and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove smaltRemove smalt Configurations and Data
To remove smalt configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge smaltRemove smalt configuration, data, and all of its dependencies
We can use the following command to remove smalt configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge smaltDependencies
smalt have the following dependencies:
References
Summary
In this tutorial we learn how to install smalt package on Kali Linux using different package management tools: apt, apt-get and aptitude.