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