NAME

       pbdagcon - sequence consensus using directed acyclic graphs

DESCRIPTION

       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(1) 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(1)  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,  pre-assembly  and  a  work  around  to
       generate consensus from intermediate Celera Assembler outputs.

OPTIONS

       A summary of options is available from the program's help menu.

       --help Show summary of options.

SEE ALSO

       blasr(1),
       /usr/share/doc/pbdagcon/examples

                                          December 2015                               PBDAGCON(1)