DNA Integrity in Whole Genome Sequencing

Question

[rizky_dsatrio]

How important DNA integrity in the whole genome resequencing? If the early step of the library construction is DNA fragmentation (sonication), why NGS companies reject the sample that has degradation, or fragment size lower than 20kb?

[h.mon]

I believe companies do not "reject", they probably warn the client the quality of sequencing and downstream analyses may be negatively affected. If the client then chooses to proceed, companies will proceed.

[rizky_dsatrio]

Dear h.mon

Thank you for your comment. How do you think about the downstream analysis that may be affected by low integrity DNA? If sonication step produces fragmented (small-size) DNA, why low integrity DNA can affect the sequencing quality or downstream analysis?

Regards