How To Install select_all_rbcontig.pl on Kali Linux

One-liner install command

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

sudo apt-get update && sudo apt -y install bio-rainbow

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

What is select_all_rbcontig.pl and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Kali Linux. This guide was written specifically with a server running Kali Linux 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 select_all_rbcontig.pl on Kali Linux. 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 select_all_rbcontig.pl 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 select_all_rbcontig.pl using apt by running the following command:

sudo apt -y install bio-rainbow

Install select_all_rbcontig.pl using apt

Because select_all_rbcontig.pl is available in Kali Linux’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 select_all_rbcontig.pl using apt by running the following command:

sudo apt -y install bio-rainbow

Install select_all_rbcontig.pl 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 Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install select_all_rbcontig.pl by running the following command:

sudo aptitude -y install bio-rainbow

How to upgrade (update) a single package select_all_rbcontig.pl 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 select_all_rbcontig.pl, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install bio-rainbow

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 bio-rainbow

How To Uninstall select_all_rbcontig.pl from Kali Linux

To uninstall only the select_all_rbcontig.pl package you can execute the following command:

sudo apt-get remove bio-rainbow

Uninstall select_all_rbcontig.pl and all its dependencies

To uninstall select_all_rbcontig.pl and its dependencies that are no longer needed by Kali Linux, you can use the command below:

sudo apt-get -y autoremove bio-rainbow

Remove select_all_rbcontig.pl with all configurations and data

To remove select_all_rbcontig.pl configuration and data from your system you can run the following purge command:

sudo apt-get -y purge bio-rainbow

Remove select_all_rbcontig.pl completely (configurations, data and all of its dependencies)

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

sudo apt-get -y autoremove --purge bio-rainbow

Extra info and code examples

Efficient tool for clustering and assembling short reads, especially for RAD. Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide potential groups into haplotypes in a top-down manner. long a guided tree, it iteratively merges sibling leaves in a bottom-up manner if they are similar enough. Here, the similarity is defined by comparing the 2nd reads of a RAD segment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on simulation and a real guppy RAD-seq data, it is shown that Rainbow is more competent than the other tools in dealing with RAD-seq data.

Conclusion

You now have a full guide on how to install select_all_rbcontig.pl using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the select_all_rbcontig.pl from Kali Linux.

See also: