Is there a safe catch-all adapter sequence for trimming?

I see no benefit to using MarkIlluminaAdapters, replace it completely.More

For clarity, are you suggesting it's better to switch over completely to this recommended set of tools, or are you simply introducing the possibility of using fastp to determine the adapters (or extract the list from trim galore)? One benefit of using MarkIlluminaAdapters is that it simply "marks" the sequences using More

If you want that just use an aligner with soft clipping. Note also that few aligners support SAM input.More

Lol, I think I'll start calling mappers "read slingers" :winking_face: To be serious though, it's More

for a conscientious bioinformatician to store reads in SAM (et al.) format at every stage (raw unaligned, QC'd, aligned, aligned post-processed, etc.) in a way that preserves the original raw sequence unambiguously. In practice though, it will be problematic since many tools are not designed with this paradigm in mind. It would take years to get everyone on the same page, if indeed it's even possible to do so.More