I want to know the details of pair-end sequencing, especially how the products of the first sequencing are removed.
I understand that pair-end sequencing is a method of DNA sequencing that can simultaneously sequence both ends of a DNA fragment, obtaining more information and higher accuracy. I also know that pair-end sequencing involves three steps: library preparation, amplification and sequencing, and alignment and analysis. However, I am confused about the following points:
How are the products of the first sequencing removed? I know that there are some methods, such as using double-strand specific nuclease (DSN). But if a double-stranded DNA-specific restriction enzyme is used, how can the template for the second sequencing be protected from being destroyed, since it is also a part of the double-stranded DNA?
I would appreciate it if someone could explain these points to me in detail or provide some references for further reading. Thank you very much.
Thanks to @rfran010 's answer, it seems that I have confused the product of the first sequencing with the PCR process in preparation for the second sequencing. The products of the first sequencing should be easily removed because there is no covalent connection.
So the question is, actually, how did the template of the first round be removed here? Through specific restriction enzymes?