Package: pbdagcon (0.3+git20161121.0000000+ds-1.1)

[ Source: pbdagcon  ]

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

• dep: libc6 (>= 2.17)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libgcc1 (>= 1:3.0)

  GCC support library

• dep: libhdf5-103

  Hierarchical Data Format 5 (HDF5) - runtime files - serial version

• dep: libhdf5-cpp-103 (>= 1.8.13)

  Hierarchical Data Format 5 (HDF5) - C++ libraries

• dep: libhts2 (>= 1.0)

  C library for high-throughput sequencing data formats

• dep: libpbbam0.19.0 (>= 0.19.0+dfsg)

  Pacific Biosciences binary alignment/map (BAM) library

• dep: libpbseq

  library for analyzing PacBio sequencing data

• dep: libstdc++6 (>= 6)

  GNU Standard C++ Library v3

• dep: zlib1g (>= 1:1.1.4)

  compression library - runtime

• sug: blasr

  mapping single-molecule sequencing reads

Download pbdagcon

Download for all available architectures

Architecture	Package Size	Installed Size	Files
arm64	285.0 kB	1,078.0 kB	[list of files]