Can chimeras be formed without adapter sequences?

[Jonathan-Abrahams]

Hi,

I have a general question about Nanopore sequencing, based on the documentation of Badread. I hope this is the most appropriate way to ask this!

In the Chimera section of the documentation of Badread, the following is mentioned:

"If you are using start/end adapters, they will sometimes (but not always) be added between the fragments."

Would you have any citations for this or could you explain why this would be the case in real data?

My best guess is that to be sequenced a read MUST have an adapter. In a chimera though, only the first DNA fragment of the chimera must have an adapter and therefore if a DNA fragment that escaped the adapter adding stage is joined to the first fragment this would produce a 'scar-less' chimera. Is this correct?

Thanks for your help,

Jonathan