To cite outbreaker:

  Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N
  (accepted).  Bayesian reconstruction of disease outbreaks by
  combining epidemiologic and genomic data. PLoS Computational Biology.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data},
    journal = {PLoS Computational Biology},
    year = {accepted},
    author = {Jombart T and Cori A and Didelot X and Cauchemez S and Fraser C and Ferguson N},
  }