How to Install and Uninstall pbdagcon Package on Ubuntu 16.04 LTS (Xenial Xerus)

Last updated: May 12,2024

1. Install "pbdagcon" package

Learn how to install pbdagcon on Ubuntu 16.04 LTS (Xenial Xerus)


    
        
            $
        

        
            
                sudo apt update
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt install
            
                        
                pbdagcon
            
                    
    
    Copied

2. Uninstall "pbdagcon" package

Please follow the instructions below to uninstall pbdagcon on Ubuntu 16.04 LTS (Xenial Xerus):


    
        
            $
        

        
            
                sudo apt remove
            
                        
                pbdagcon
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
    Copied

3. Information about the pbdagcon package on Ubuntu 16.04 LTS (Xenial Xerus)

Package: pbdagcon
Priority: optional
Section: universe/science
Installed-Size: 526
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Architecture: amd64
Version: 0~20151114+git1d12e13+ds-2
Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.4), libstdc++6 (>= 5.2), libpbdata, libblasr
Suggests: blasr
Filename: pool/universe/p/pbdagcon/pbdagcon_0~20151114+git1d12e13+ds-2_amd64.deb
Size: 191638
MD5sum: b14b35e7c976b1830c3bd48139eb9445
SHA1: f22f04b5598c341c4e19e9c0f678ed19c08a678a
SHA256: 6c517547e9c87b9b0648f80508dc29c2be8da0aa66115bbc85657434a71b1c7e
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.
.
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.
.
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.
.
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
Homepage: https://github.com/PacificBiosciences/pbdagcon
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Origin: Ubuntu