Illumina WGS of clinical M. tuberculosis isolates
Each isolate was thawed and subcultured on LJ and a big loop of colonies were lysed with lysozyme and proteinase K to obtain DNA using CTAB/Chloroform extraction and ethanol precipitation. DNA was sheared into ~_250_bp fragments using a Covaris sonicator (Covaris,Inc.), and prepared using the TruSeq Whole-Genome Sequencing DNA sample preparation kit (Illumina, Inc.). Samples were sequenced on an Illumina HiSeq 2500 sequencer. Paired-end reads of length 125_bp were collected. Base-calling was performed using HCS 2.2.58 and RTA 1.18.64 software (Illumina, Inc.)