How To Install spades-bwa on Ubuntu 21.04

One-liner install command

For those in a hurry, here's a one-line installation command:

sudo apt-get update && sudo apt -y install spades

But if you are interested in the detailed steps with descriptions, the following information is for you.

What is spades-bwa and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Ubuntu 21.04. This guide was written specifically with a server running Ubuntu 21.04 in mind, although it should also work on older, supported versions of the operating system.

Also, make sure you are running a regular, non-root user with sudo privileges configured on your server. When you have an account available, log in as your non-root user to begin.

There are several ways to install spades-bwa on Ubuntu 21.04. You can use (links are clickable):

In the following sections, we will describe each method in detail. You can choose one of them or refer to the recommended one.

Install spades-bwa using apt-get

First, update apt database with apt-get using the following command.

sudo apt-get update

After updating apt-get database, You can install spades-bwa using apt by running the following command:

sudo apt -y install spades

Install spades-bwa using apt

Because spades-bwa is available in Ubuntu 21.04’s default repositories, it is possible to install it from these repositories using the apt packaging system.

To begin, update apt database with apt using the following command.

sudo apt update

After updating apt database, You can install spades-bwa using apt by running the following command:

sudo apt -y install spades

Install spades-bwa 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 21.04. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install spades-bwa by running the following command:

sudo aptitude -y install spades

How to upgrade (update) a single package spades-bwa using apt-get?

First, you will need to update packages index. Run update command as usual:

sudo apt-get update

Next, to upgrade only the spades-bwa, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install spades

Note that this command will not install any new packages! If you wish to install the package if it doesn't exist you may leave out --only-upgrade part.

sudo apt-get install spades

How To Uninstall spades-bwa from Ubuntu 21.04

To uninstall only the spades-bwa package you can execute the following command:

sudo apt-get remove spades

Uninstall spades-bwa and all its dependencies

To uninstall spades-bwa and its dependencies that are no longer needed by Ubuntu 21.04, you can use the command below:

sudo apt-get -y autoremove spades

Remove spades-bwa with all configurations and data

To remove spades-bwa configuration and data from your system you can run the following purge command:

sudo apt-get -y purge spades

Remove spades-bwa completely (configurations, data and all of its dependencies)

And lastly, you can run the next command to remove absolutely everything related to spades-bwa package, e.g.: configurations, data and all of its dependencies. Just use this command:

sudo apt-get -y autoremove --purge spades

Extra info and code examples

The SPAdes – St. Petersburg genome assembler is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio and Sanger reads. You can also provide additional contigs that will be used as long reads.

Conclusion

You now have a full guide on how to install spades-bwa using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the spades-bwa from Ubuntu 21.04.

See also: