This is the command pbdagcon that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
Use pbdagcon online using onworks.net services
