Marcel Martin

As I mentioned in #676, the trimming algorithm is copied from BWA and should not be changed directly. A new option would be needed, and also some test cases.

Hi, thanks for the suggestion. Can you explain a bit why you think this would be useful? I haven’t encountered a situation where that would make so much sense, mostly...

Barcodes in data I have worked with were usually directly at the 5' end, and Cutadapt offers [anchored 5' adapters](https://cutadapt.readthedocs.io/en/stable/guide.html#anchored-5adapters) for these. If you need to be a bit more...

I’m not familiar with how sn/scATAC-seq data looks and admit I don’t have the time to find this out myself right now. I’ll comment a bit based on what I...

I would like to understand what exactly you would need Cutadapt to do. Could you provide a (toy) example of an input read triple (R1, R2, I1) plus the expected...

Thanks for the feedback! As a workaround, you can swap the R1 and R2 input and output files and the read-specific options (such as `-a` ↔ `-A` and `-m` ↔...

Please see here: https://cutadapt.readthedocs.io/en/stable/guide.html#filtering-paired Happy to answer in more detail if needed when I'm back from vacation next week.

Hi, that’s interesting. By default, the largest FASTQ record may have 4 million bytes. This includes the quality values, so the maximum read length is about 2 Mbp. I thought...

Awesome! Let me re-open this until I’ve found a more permanent solution. Maybe I can make the buffer size dynamic or so.

The strategy is good, but just ignoring the exception and re-trying will lose the contents of the buffer. This would have to be done within `read_chunks` directly.