Introduction
In this tutorial we learn how to install baitfisher on Kali Linux.
What is baitfisher
baitfisher is:
The BaitFisher package consists of two programs: BaitFisher and BaitFilter.
BaitFisher was been designed to construct hybrid enrichment baits from
multiple sequence alignments (MSAs) or annotated features in MSAs. The main
goal of BaitFisher is to avoid redundancy in the construction of baits by
designing fewer baits in conserved regions of the MSAs and designing more baits
in variable regions. This makes use of the fact that hybrid enrichment baits
can differ to some extends from the target region, which they should capture
in the enrichment procedure.
By specifying the allowed distance between baits and the sequences in the MSAs
the user can control the allowed bait-to-target distance and the degree of
reduction in the number of baits that are designed.
See the BaitFisher paper for details.
BaitFilter was designed (i) to determine whether baits bind unspecifically to
a reference genome, (ii) to filter baits that only have partial length matches
to a reference genome, (iii) to determine the optimal bait region in a MSA and
to convert baits to a format that can be uploaded at a bait constructing
company. The optimal bait region can be the most conserved region in the MSA
or the region with the highest number of sequences without gaps or ambiguous
nucleotides.
There are three methods to install baitfisher 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 baitfisher Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install baitfisher using apt-get by running the following command:
sudo apt-get -y install baitfisherInstall baitfisher Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install baitfisher using apt by running the following command:
sudo apt -y install baitfisherInstall baitfisher 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 baitfisher using aptitude by running the following command:
sudo aptitude -y install baitfisher
How To Uninstall baitfisher on Kali Linux
To uninstall only the baitfisher package we can use the following command:
sudo apt-get remove baitfisher
Uninstall baitfisher And Its Dependencies
To uninstall baitfisher and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove baitfisher
Remove baitfisher Configurations and Data
To remove baitfisher configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge baitfisher
Remove baitfisher configuration, data, and all of its dependencies
We can use the following command to remove baitfisher configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge baitfisher
Dependencies
baitfisher have the following dependencies:
References
Summary
In this tutorial we learn how to install baitfisher package on Kali Linux using different package management tools: apt, apt-get and aptitude.
