Marcel Martin

Hi, thank you for the suggestion, and I agree this behavior would be more consistent with what the other options do. However, I needed to implement it this way for...

You need to create the `barcodes_fwd.fasta` and `barcodes_rev.fasta` files. Read also the [general section about demultiplexing in the documentation](https://cutadapt.readthedocs.io/en/stable/guide.html#demultiplexing), which describes how such a `barcodes.fasta` file needs to look.

Indeed a nice improvement in readability! Awesome that it’s possible to trust the compiler here.

Hi, in case it is still relevant: You can provide multiple primers/adapters with the same name. So something like this: ``` >341F (sequence of 341F) >341F (sequence of 341Fb) ```...

Getting back to this: I don’t understand the last question. If still relevant, can you re-phrase?

> If in a situation in which I have heterogeneity spacers+primers in my paired-end data, like: > > ``` > Bacterial region V3-V4: > 341F (5´-CCTACGGGNGGCWGCAG-3´) > 341Fb (5´-TCCTACGGGNGGCWGCAG-3´) >...

Hi and thanks for doing this analysis. I’ve so far only had time to look into the first issue, and I think it’s a bug that the very first k-mer...

> To a certain extent, it doesn't necessarily matter exactly which precise definition you use for syncmers, so long as the implementation expresses that definition on all code paths. Yes,...

After a couple of measurements on a different (10 years younger) machine, I *can* measure a difference - this PR makes mapping-only mode about 2% faster. (This comes at the...

> Great! Don't we anyway have B top bits available to store other things because of our prefix vector? This depends of course on that the bit is added after...