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)