Skip to content
Sections
>> Trisquel >> Packages >> aramo >> science >> pbdagcon
etiona  ] [  nabia  ] [  aramo  ]
[ Source: pbdagcon  ]

Package: pbdagcon (0.3+git20180411.c14c422+dfsg-8)

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.

Other Packages Related to pbdagcon

  • depends
  • recommends
  • suggests
  • dep: libblasr5.3.5 (>= 5.3.5+dfsg)
    tools for aligning PacBio reads to target sequences
  • dep: libc6 (>= 2.34)
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
  • dep: libgcc-s1 (>= 3.3.1)
    GCC support library
  • dep: libpbseq (>= 5.3.5+dfsg-4~)
    library for analyzing PacBio sequencing data
  • dep: libstdc++6 (>= 12)
    GNU Standard C++ Library v3
  • sug: blasr
    mapping single-molecule sequencing reads

Download pbdagcon

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 269.2 kB860 kB [list of files]
arm64 252.3 kB776 kB [list of files]
ppc64el 276.9 kB1008 kB [list of files]