How to Install and Uninstall baitfisher Package on Ubuntu 21.10 (Impish Indri)

Last updated: November 26,2024

1. Install "baitfisher" package

This guide covers the steps necessary to install baitfisher on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                baitfisher
            
                    
    
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2. Uninstall "baitfisher" package

This tutorial shows how to uninstall baitfisher on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                baitfisher
            
                    
    
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            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the baitfisher package on Ubuntu 21.10 (Impish Indri)

Package: baitfisher
Architecture: amd64
Version: 1.2.7+git20190123.241d060+dfsg-1
Priority: optional
Section: universe/science
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 638
Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2)
Filename: pool/universe/b/baitfisher/baitfisher_1.2.7+git20190123.241d060+dfsg-1_amd64.deb
Size: 194244
MD5sum: 36b4afcfd2333ed343ab4597bf083142
SHA1: 6d317bca9810f69bcfd30371392868cbad01450e
SHA256: e6f1cfd06d933c5989aefb280b78bc37bf2ac3cd35423e40289b4b85fb49bc25
SHA512: 510b4b9edc539dc965c43834432c33e136d5b93dad201a9faeb6b70730922c71e197f2f6cc287eb704209a3ae705978523fc86d4dfb76cb46cb6b121f0ec6268
Homepage: https://github.com/cmayer/BaitFisher-package
Description-en: software package for designing hybrid enrichment probes
The BaitFisher package consists of two programs: BaitFisher and BaitFilter.
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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.
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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.
Description-md5: 4f8112acea1615fb8dd7625fdf2f7898