Marcel Martin

Hm, you may have a point. I haven’t followed Atropos development, but perhaps it’s time to see whether some of the code can be re-integrated into Cutadapt. Note to myself:...

A couple of thoughts because this came up just now in #552: * This should be made to work even for linked adapters * We could enable this when `--pair-adapters`...

I tried this, but I’m not able to reproduce the problem on my test data. With issue #244 fixed, this shouldn’t happen. As a test, can you swap the R1...

I realized just now that cutadapt doesn’t report quality-trimming statistics when `--nextseq-trim` is used. This is now fixed.

Thanks for the test data. Yes, your observation is correct: Nextseq-specific quality trimming removes bases only from the 3' end. This is by design since the “dark cycles” (encoding `G`...

You’re welcome! I’ll close this issue then. Feel free to open a new one if anything else comes up.

I’ll re-open this as it appear that the `--nextseq-trim` algorithm needs to be tuned a little bit. Would you be willing to share one or two of your sequences that...

Thanks for the files. Modifying the algorithm will probably take some time, so no promises I can do this soon.

This isn’t supported at the moment. (If it gets supported, the syntax would use a comma instead of a hyphen as in `N{10,15}` because that is what is used in...

Just to clarify: What would these two reads need to look like after trimming?