How To Install shasta on Kali Linux

In this tutorial we learn how to install shasta on Kali Linux. shasta is nanopore whole genome assembly (binaries and scripts)

Introduction

In this tutorial we learn how to install shasta on Kali Linux.

What is shasta

shasta is:

De novo assembly from Oxford Nanopore reads. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.

Computational methods used by the Shasta assembler include:

  • Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads.

  • Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ?? 10).

Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers.

This package contains the executable binaries (tools) and accommodating scripts.

There are three methods to install shasta 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 shasta Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install shasta using apt-get by running the following command:

sudo apt-get -y install shasta

Install shasta Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install shasta using apt by running the following command:

sudo apt -y install shasta

Install shasta 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 shasta using aptitude by running the following command:

sudo aptitude -y install shasta

How To Uninstall shasta on Kali Linux

To uninstall only the shasta package we can use the following command:

sudo apt-get remove shasta

Uninstall shasta And Its Dependencies

To uninstall shasta and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove shasta

Remove shasta Configurations and Data

To remove shasta configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge shasta

Remove shasta configuration, data, and all of its dependencies

We can use the following command to remove shasta configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge shasta

Dependencies

shasta have the following dependencies:

References

Summary

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