Does this adapter content from fastqc to warrant trimming prior to alignment?

Question

[curious]

Hi I am looking to align some human short read WGS data with BWA-MEM prior to variant calling. I have 62 samples, each has 8 pairs of fastqs (992 fastqs total). I ran fastqc/multiqc on all of them and got this result from multiqc:

For comparison here is an individual fastqc:

Spot checking a handful of individual fastqc reports it seems the flat universal adapter line hovering around 2ish percent and that poly a line creeping up over the length of the read is pretty typical, does this require trimming prior to alignment?

According to this the threshold for warning is 5% and failure is 10%, but just wondering what the general practice is

Thanks!

Answer 1

[GenoMax]

It is an investment in time and will ensure that there is no extraneous sequence is present, if you choose to do scanning/trimming.

That said aligners should soft-clip the adapter sequence at the time of alignment, so technically you do not need to trim the data.

Note: Those sequences that show adapter starting at cycle 1 are likely all primer dimers and have no inserts.