Trimmomatic on NEBNext Ultra II FS DNA

Question

[plicht]

Hello together,

has anybody used Trimmomatic with the NEBNext Ultra II FS DNA Lib Prep Kit (NEBNext Ultra II FS DNA) together with Multiplex Oligos from NEB (e. g. Multiplex Oligos for Illumina) before? Do I need to adjust the reference adapter file of Trimmomatic? Since the adapters used by NEB are the same as of Illumina's TruSeq, I guess there is no adjustment needed. Am I right?

[benformatics]

If what you say is true then I would assume you are good to go. However, it would be good to double-check post trimming that there aren't specific oligos remaining at either read end (e.g. fastqc).