Introduction
In this tutorial we learn how to install bio-rainbow on Kali Linux.
What is bio-rainbow
bio-rainbow is:
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.
There are three methods to install bio-rainbow 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 bio-rainbow Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install bio-rainbow using apt-get by running the following command:
sudo apt-get -y install bio-rainbowInstall bio-rainbow Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install bio-rainbow using apt by running the following command:
sudo apt -y install bio-rainbowInstall bio-rainbow 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 updateAfter updating apt database, We can install bio-rainbow using aptitude by running the following command:
sudo aptitude -y install bio-rainbow
How To Uninstall bio-rainbow on Kali Linux
To uninstall only the bio-rainbow package we can use the following command:
sudo apt-get remove bio-rainbow
Uninstall bio-rainbow And Its Dependencies
To uninstall bio-rainbow and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove bio-rainbow
Remove bio-rainbow Configurations and Data
To remove bio-rainbow configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge bio-rainbow
Remove bio-rainbow configuration, data, and all of its dependencies
We can use the following command to remove bio-rainbow configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge bio-rainbow
Dependencies
bio-rainbow have the following dependencies:
References
Summary
In this tutorial we learn how to install bio-rainbow package on Kali Linux using different package management tools: apt, apt-get and aptitude.
