How To Install smalt on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 465 words
Introduction
In this tutorial we learn how to install smalt on Ubuntu.
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 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 smalt Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install smalt using apt-get by running the following command:
sudo apt-get -y install smalt
Install smalt Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install smalt using apt by running the following command:
sudo apt -y install smalt
Install smalt 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 smalt using aptitude by running the following command:
sudo aptitude -y install smalt
How To Uninstall smalt on Ubuntu
To uninstall only the smalt package we can use the following command:
sudo apt-get remove smalt
Uninstall smalt And Its Dependencies
To uninstall smalt and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove smalt
Remove smalt Configurations and Data
To remove smalt configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge smalt
Remove 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 smalt
Dependencies
smalt have the following dependencies:
References
Summary
In this tutorial we learn how to install smalt package on Ubuntu using different package management tools: apt, apt-get and aptitude.