A. Gillaspy, S. Hickmon, R. Skinner, J. Thomas, C. Nelson et al., Role of the accessory gene regulator (agr) in pathogenesis of staphylococcal osteomyelitis, Infect Immun, vol.63, pp.3373-3380, 1995.

J. Cassat, P. Dunman, F. Mcaleese, E. Murphy, S. Projan et al., Comparative Genomics of Staphylococcus aureus Musculoskeletal Isolates, Journal of Bacteriology, vol.187, issue.2, pp.576-592, 2005.
DOI : 10.1128/JB.187.2.576-592.2005

P. Olson, L. Kuechenmeister, K. Anderson, S. Daily, K. Beenken et al., Small Molecule Inhibitors of Staphylococcus aureus RnpA Alter Cellular mRNA Turnover, Exhibit Antimicrobial Activity, and Attenuate Pathogenesis, PLoS Pathogens, vol.19, issue.2, p.1001287, 2011.
DOI : 10.1371/journal.ppat.1001287.s006

S. Herbert, A. Ziebandt, K. Ohlsen, T. Schäfer, M. Hecker et al., Repair of Global Regulators in Staphylococcus aureus 8325 and Comparative Analysis with Other Clinical Isolates, Infection and Immunity, vol.78, issue.6, pp.2877-2889, 2010.
DOI : 10.1128/IAI.00088-10

M. Lohse, A. Bolger, A. Nagel, A. Fernie, J. Lunn et al., RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics, Nucleic Acids Research, vol.40, issue.W1, pp.622-627, 2012.
DOI : 10.1093/nar/gks540

A. Bankevich, S. Nurk, D. Antipov, A. Gurevich, M. Dvorkin et al., SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, issue.5, pp.455-477, 2012.
DOI : 10.1089/cmb.2012.0021

S. Nurk, A. Bankevich, D. Antipov, A. Gurevich, A. Korobeynikov et al., Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products, Journal of Computational Biology, vol.20, issue.10, pp.714-737, 2013.
DOI : 10.1089/cmb.2013.0084

F. Nadalin, F. Vezzi, and A. Policriti, GapFiller: a de novo assembly approach to fill the gap within paired reads, BMC Bioinformatics, vol.13, issue.Suppl 14, pp.1471-2105, 2012.
DOI : 10.1016/0022-2836(81)90087-5

M. Boetzer and W. Pirovano, Toward almost closed genomes with GapFiller, Genome Biology, vol.13, issue.6, 2012.
DOI : 10.1186/gb-2009-10-10-r103

S. Angiuoli, A. Gussman, W. Klimke, G. Cochrane, D. Field et al., Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation, OMICS: A Journal of Integrative Biology, vol.12, issue.2, pp.137-1410017, 2008.
DOI : 10.1089/omi.2008.0017

Y. Zhou, Y. Liang, K. Lynch, J. Dennis, and D. Wishart, PHAST: A Fast Phage Search Tool, Nucleic Acids Research, vol.39, issue.suppl, pp.347-352, 2011.
DOI : 10.1093/nar/gkr485

I. Grissa, G. Vergnaud, and C. Pourcel, CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic Acids Research, vol.35, issue.Web Server, pp.52-57, 2007.
DOI : 10.1093/nar/gkm360

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