How To Install smalt-examples on Debian 10
Introduction
In this tutorial we learn how to install smalt-examples
on Debian 10.
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 Debian 10. 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 Debian. 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 Debian 10
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 Debian 10, 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 Debian 10 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 Debian 10 using different package management tools: apt
, apt-get
and aptitude
.