fastp not removing all Illumina universal adapter sequences as indicated by FastQC

[luckyvivi]

fastp not removing all Illumina universal adapter sequences as indicated by FastQC

[luckyvivi]

SRR18278237 (1).fastp.zip

[nreid]

I have a similar issue, but with Nextera adapters. fastp says no contamination, FastQC says nextera, up to 10% by the read end. Even when I supply the Nextera fasta file (the one provided by trimmomatic) virtually no trimming happens.

Trimmomatic with ILLUMINACLIP:"${ADAPTERS}":2:30:10 SLIDINGWINDOW:4:25 MINLEN:45 and drops 7.25% of all reads.

This isn't a perfect comparison, I think fastp default min window Q is 20, not 25, but still. Something seems off here. I'm using v0.23.2.

[realzhang]

Same problem. Any suggestion is welcome. Thanks!

[nreid]

I switched back to fastqc/trimmomatic/fastqc. I'm removing fastp from my workflows.

There are also a couple concerning GitHub issues about reproducibility. I like the tool but I can't use it if these things aren't resolved.