title: Genome of Clostridium difficile: strain 008
design: For sequencing, the 12 DNA samples were quantified on the Qubit fluorometer (Invitrogen), using the Qubit dsDNA high-sensitivity assay (Invitrogen), following the company's protocol. After DNA quantification, the libraries were prepared with the Nextera XT DNA Library Preparation Kit (Illumina), according to the manufacturer's protocol. The C. difficile strain was identified with a index of the Nextera XT Index Kit (Illumina), so that the samples could be mixed and sequenced simultaneously and identified in the post-sequencing bioinformatics data analysis. The libraries were sequenced using the MiSeq Reagent Kit v3 (Illumina), following the manufacturer's protocol, through the MiSeq System (Illumina) platform.