a doubt about the quality plot

Hello guys, I hope you are all well.

I'm running version 2021.2 on VirtualBox.
I just used the vsearch join-pairs plugin on paired end reads. In the quality plot, can the area indicated with the circle, with the highest score, represent the overlap region?

Thank you very much.

Best regards,



Your intuition that this region represents the overlap is correct. There is a previous discussion about this topic here. Mentioned in the preceding thread is this article from Bioinformatics that provides a more rigorous treatment of the subject.


@Keegan-Evans, thank you very much, and sorry for the silly question, but I did a quick search on the forum and couldn’t find anything about it. I was worried it might be something weird from the sequencing.

Best reagards!

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@Andre_Pegoraro thanks for doing a search first! That said, there are a lot of posts to try to dig through and we are happy to point you in the right direction. The forum is a great place to reach out and make sure your assumptions are correct, we are all here to make sure great quality is getting done :grinning:

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