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)