Use of --detect_adapter_for_pe and order of adapter removal

Question

[SergeW]

Hi,

Currently, I am using fastp (v0.23.2) to remove adapter-readthrough from paired-end Illumina read datasets.

In case of providing both --detect_adapter_for_pe and --adapter_fasta as parameters, in what order are these parameters executed and how does --detect_adapter_for_pe exactly work? Does it use a built-in list of adapter sequences to check for, which is the method as for providing a separate FASTA file?

I assume it is adapter trimming in the following order (having read the fastp GitHub page):

1. Overlap read analysis If no overlap was found, perform following steps;
2. Trim using --detect_adapter_for_pe (Built-in list of known Illumina adapters?)
3. Trim using provided FASTA file containing one or multiple adapter sequences

Could someone please enlighten me how the adapter removal options work and when to explicitly provide the tool FASTA sequences. Does option 1 for example work well on datasets from other sequencing instruments (e.g. BGI/MGI)?

Thanks in advance.