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

Last updated: May 12,2024

1. Install "pbdagcon" package

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


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                pbdagcon
            
                    
    
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2. Uninstall "pbdagcon" package

This guide let you learn how to uninstall pbdagcon on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                pbdagcon
            
                    
    
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            $
        

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

Package: pbdagcon
Architecture: amd64
Version: 0.3+git20180411.c14c422+dfsg-1build3
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: 1292
Depends: libblasr5.3.4 (>= 5.3.4+dfsg), libc6 (>= 2.14), libgcc-s1 (>= 3.4), libstdc++6 (>= 9), libpbseq (>= 5.3.3)
Suggests: blasr
Filename: pool/universe/p/pbdagcon/pbdagcon_0.3+git20180411.c14c422+dfsg-1build3_amd64.deb
Size: 351428
MD5sum: ba78bb5e21167b38d2f727e46d63e55d
SHA1: f6d9d2f67ec305300251073493a680d8b5ec2c57
SHA256: 025efda21aa805a79a5bf64bf4ed141e98b734a9469d1c094c30a2e70cda270c
SHA512: 61ccf11b7e1afaefb037fe9cd94efd8ce4336983c7fc455dcb1adec892f01bbb0a0224febb5809c05932fac1fd18978596544fdc5db649e3e08a5f4fe3ec7514
Homepage: https://github.com/PacificBiosciences/pbdagcon
Description-en: sequence consensus using directed acyclic graphs
pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus)
which is a sequence consensus algorithm based on using directed acyclic
graphs to encode multiple sequence alignment.
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It uses the alignment information from blasr to align sequence reads to a
"backbone" sequence. Based on the underlying alignment directed acyclic graph
(DAG), it will be able to use the new information from the reads to find the
discrepancies between the reads and the "backbone" sequences. A dynamic
programming process is then applied to the DAG to find the optimum sequence
of bases as the consensus. The new consensus can be used as a new backbone
sequence to iteratively improve the consensus quality.
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While the code is developed for processing PacBio(TM) raw sequence data,
the algorithm can be used for general consensus purpose. Currently, it only
takes FASTA input. For shorter read sequences, one might need to adjust the
blasr alignment parameters to get the alignment string properly.
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The code and the underlying graphical data structure have been used for some
algorithm development prototyping including phasing reads and pre-assembly.
Description-md5: 95465f5fc6fbaa2db477a48c78b7cd82