ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction

@article{Bodily2015ScaffoldScaffolderSC,
  title={ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction},
  author={Paul Bodily and M. Stanley Fujimoto and Quinn Snell and Dan Ventura and Mark J. Clement},
  journal={Bioinformatics},
  year={2015},
  volume={32 1},
  pages={
          17-24
        }
}
MOTIVATION The contig orientation problem, which we formally define as the MAX-DIR problem, has at times been addressed cursorily and at times using various heuristics. In setting forth a linear-time reduction from the MAX-CUT problem to the MAX-DIR problem, we prove the latter is NP-complete. We compare the relative performance of a novel greedy approach with several other heuristic solutions. RESULTS Our results suggest that our greedy heuristic algorithm not only works well but also… CONTINUE READING

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