Whole genome next generation sequencing of Mycobacterium tuberculosis: sputum clinical  isolate
The DNA extracted from the isolates was sequenced in Illumina Miseq (Illumina, USA) with a minimum coverage of 100X.  The DNA was purified and tagmented using the NEXTERA XT transposome (Illumina, USA). The tagmented DNA was amplified through a limited cycle amplified program along with index primers (N7XX/i7, S5XX/i5) (Illumina, USA), followed by PCR clean-up using AMPure XP beads and Resuspension buffer (Illumina, USA) to provide a size selection by removing very short library fragments. Library normalization was carried out to ensure more equal library. The prepared library was then mixed with 4nM PHIX control (Illumina, USA). The final library was pooled and added to the flow cell and loaded into the Illumina Miseq machine.