How To Install python3-shasta on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 464 words

Introduction

In this tutorial we learn how to install python3-shasta on Ubuntu.

What is `python3-shasta`

python3-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 dynamic library that can be interfaced and imported within Python.

There are three methods to install python3-shasta 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 python3-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 python3-shasta using apt-get by running the following command:

sudo apt-get -y install python3-shasta

Install python3-shasta Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install python3-shasta using apt by running the following command:

sudo apt -y install python3-shasta

Install python3-shasta 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 python3-shasta using aptitude by running the following command:

sudo aptitude -y install python3-shasta

How To Uninstall python3-shasta on Ubuntu

To uninstall only the python3-shasta package we can use the following command:

sudo apt-get remove python3-shasta

Uninstall python3-shasta And Its Dependencies

To uninstall python3-shasta and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove python3-shasta

Remove python3-shasta Configurations and Data

To remove python3-shasta configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge python3-shasta

Remove python3-shasta configuration, data, and all of its dependencies

We can use the following command to remove python3-shasta configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge python3-shasta

Dependencies

python3-shasta have the following dependencies:

References

python3-shasta website

Summary

In this tutorial we learn how to install python3-shasta package on Ubuntu using different package management tools: apt, apt-get and aptitude.