If you found this pipleine useful, please cite the following papers:

Puritz, J. B., Hollenbeck, C. M., Gold, J. R. dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ 2:e431 LINK

Puritz, J.B., Matz, M. V., Toonen, R. J., Weber, J. N., Bolnick, D. I., Bird, C. E. Comment: Demystifying the RAD fad. Molecular Ecology 23: 5937–5942. doi: 10.1111/mec.12965 LINK