M. bovis BCG
Total genomic DNA was extracted using the geneLEAD VIII (Diagenode Diagnostics) automated DNA extractor from isolate grown on Lwenstein-Jensen medium. Preparation of paired-end libraries using an Illumina Nextera XT kit (Illumina, San Diego, CA, USA) and Illumina NextSeq 550 WGS sequencing were done by the sequencing platform P2M-PIBnet (Institut Pasteur, Paris, France) following manufacturers recommendations