How To Install smalt-examples on Kali Linux

Introduction

In this tutorial we learn how to install smalt-examples on Kali Linux.

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 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-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 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 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 Kali Linux

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 Kali Linux, 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 Kali Linux 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

• smalt-examples website

Summary

In this tutorial we learn how to install smalt-examples package on Kali Linux using different package management tools: apt, apt-get and aptitude.