How To Install baitfisher on Debian 10

In this tutorial we learn how to install baitfisher on Debian 10. baitfisher is software package for designing hybrid enrichment probes

Introduction

In this tutorial we learn how to install baitfisher on Debian 10.

What is baitfisher

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 ways to install baitfisher on Debian 10. 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 update

After updating apt database, We can install baitfisher using apt-get by running the following command:

sudo apt-get -y install baitfisher

Install 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 baitfisher

Install baitfisher 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 Debian. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install baitfisher using aptitude by running the following command:

sudo aptitude -y install baitfisher

How To Uninstall baitfisher on Debian 10

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 Debian 10, we can use the command below:

sudo apt-get -y autoremove baitfisher

Remove baitfisher Configurations and Data

To remove baitfisher configuration and data from Debian 10 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

References

Summary

In this tutorial we learn how to install baitfisher on Debian 10 using different package management tools like apt, apt-get and aptitude.