How To Install smalt-examples on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 475 words
Introduction
In this tutorial we learn how to install smalt-examples on Ubuntu.
What is smalt-examples
smalt-examples 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.
This package contains example data and a test suite to test the data.
There are three methods to install smalt-examples 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-examples 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-examples using apt-get by running the following command:
sudo apt-get -y install smalt-examples
Install smalt-examples Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install smalt-examples using apt by running the following command:
sudo apt -y install smalt-examples
Install smalt-examples 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-examples using aptitude by running the following command:
sudo aptitude -y install smalt-examples
How To Uninstall smalt-examples on Ubuntu
To uninstall only the smalt-examples package we can use the following command:
sudo apt-get remove smalt-examples
Uninstall smalt-examples And Its Dependencies
To uninstall smalt-examples and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove smalt-examples
Remove smalt-examples Configurations and Data
To remove smalt-examples configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge smalt-examples
Remove smalt-examples configuration, data, and all of its dependencies
We can use the following command to remove smalt-examples configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge smalt-examples
Dependencies
smalt-examples have the following dependencies:
References
Summary
In this tutorial we learn how to install smalt-examples package on Ubuntu using different package management tools: apt, apt-get and aptitude.