How To Install shasta on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 454 words
Introduction
In this tutorial we learn how to install shasta on Ubuntu.
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 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 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 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 shasta using aptitude by running the following command:
sudo aptitude -y install shasta
How To Uninstall shasta on Ubuntu
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 Ubuntu, we can use the command below:
sudo apt-get -y autoremove shasta
Remove shasta Configurations and Data
To remove shasta configuration and data from Ubuntu 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 Ubuntu using different package management tools: apt, apt-get and aptitude.