Literature/Papers

Genome Assembly

• Zerbino, D. R., & Birney, E. (2008). Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18(5), 821–829. http://doi.org/10.1101/gr.074492.107

Molecular Typing

• Maiden, M. C., van Rensburg, M. J. J., Bray, J. E., Earle, S. G., Ford, S. A., Jolley, K. A., & McCarthy, N. D. (2013). MLST revisited: the gene-by-gene approach to bacterial genomics. Nature Reviews Microbiology.
• MacCannell, D. (2013). Bacterial strain typing. Clinics in laboratory medicine, 33(3), 629-650.
• Pettengill, J. B., Luo, Y., Davis, S., Chen, Y., Gonzalez-Escalona, N., Ottesen, A., ... & Strain, E. (2014). An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella. PeerJ, 2, e620.
• Inouye, M., Dashnow, H., Raven, L. A., Schultz, M. B., Pope, B. J., Tomita, T., ... & Holt, K. E. (2014). SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. bioRxiv, 006627.