If you are working with Avogadro, and need to reference it please use:

M. D. Hanwell, D. E. Curtis, D. C. Lonie, T. Vandermeersch, E. Zurek, and G. R. Hutchison, Avogadro: An Advanced Semantic Chemical Editor, Visualization, and Analysis Platform, J. Chem. Inf., 4 (17), (2012).

Another recent publication that might be of interest is:

W. A. de Jong, A. M. Walker, M. D. Hanwell, From Data to Analysis: Linking NWChem and Avogadro with the Syntax and Semantics of Chemical Markup Language, J. Chem. Inf., 5 (25), (2013).