We plan perform Mycobacterium tuberculosis whole genome sequencing of about 1,000 samples, now we're assessing different DNA extraction ways. The first results we got (picture joined) have destabilized me.

CTAB protocol vs Omega DNA extraction kit:

* electrophoresis gel shows smears (right image, degraded DNA) with Omega kit than CTAB (center view);

* we got higher DNA amount with CTAB but the average coverage is very low (we used CLC Workbench software (Qiagen), this is not the case with Omega kit where the trend is inverted. We do not plan to analyze our NGS data with that software in our study.

--> What's wrong? Why those unexpected results?

[Could someone recommend to me a working protocol that they are using or they used?] -- NGS