How To Install smalt on Debian 11

In this tutorial we learn how to install smalt on Debian 11. smalt is Sequence Mapping and Alignment Tool

Introduction

In this tutorial we learn how to install smalt on Debian 11.

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 Debian 11. 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 Debian. 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 Debian 11

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 Debian 11, we can use the command below:

sudo apt-get -y autoremove smalt

Remove smalt Configurations and Data

To remove smalt configuration and data from Debian 11 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 Debian 11 using different package management tools: apt, apt-get and aptitude.