Marcel Martin

Oh, you’re calling `_adapter_statistics_as_json` with `one_line=False`. Your suggested fix is not correct because `error_lengths` needs to be `null` when not available as [documented](https://cutadapt.readthedocs.io/en/stable/reference.html#json-report-format). I think the correct fix is to...

What type of library is this? Is this from whole-genome sequencing? What you’re describing is the Illumina read layout for a TruSeq dual index library, see https://teichlab.github.io/scg_lib_structs/methods_html/Illumina.html. Maybe you can...

Just use the command exactly as written. The adapters are already the correct ones.

Hi, the adapter sequences you give seem to be the sequencing primers. They need to be added to the DNA fragments so that the sequencing process can start, but you...

Hi, can you please clarify how your reads look? That is, where exactly are the indices in the read? Do the reads start with the index sequence? If so, you...

Hi, so do I understand correctly that you use strobealign (i.e. link to salib) from your own project’s `CMakeLists.txt`? What do you suggest we could change on our side to...

I’d tend to say that this sounds more like something that should be solved within samtools and not within each individual read mapper. Is there precedence for such an option...

Hi, I’ve run our benchmark on this commit and the previous one and don’t see any difference, not in accuracy but also not in runtime: * [ends-se-time.pdf](https://github.com/user-attachments/files/23121879/ends-se-time.pdf) * [ends-se-accuracy.pdf](https://github.com/user-attachments/files/23121878/ends-se-accuracy.pdf) I...

Hi, I suggest you run `strobealign` with the option `-v`. Then after it has read in the reference FASTA, there will be a line like this: ``` Estimated total memory...

The amount of memory is the same. There are some ideas for splitting the index into smaller chunks, but that is not implemented, yet. So the above numbers that @ksahlin...