Mick - 2019-12-28

Hi, thank you for all the work you put in BBmap.
I'm looking for a paired-end read merger, and I came across bbmerge.sh

What I need is currently not supported I think, but maybe it could be added in the future?

I have ultra-deep sequencing data for a 100bp region. The size of the DNA-fragments was short, so that forward and reverse read both cover the full 100bp. I would like to merge forward and reverse reads for this 100bp region and only keep matching bases, all non-matching bases should be replaced with Ns.

As far as I can tell there is no tool available right now, that does this. I think bbmerge is pretty close and could probably be adapted with a few lines of code. It would help me out a lot. Thank you.