As relatively new within the bioinformatics world, I am a bit confused when it comes to adapter trimming - and want to get a better understanding. At the moment I am working with PE reads generated on a NextSeq 500 - and I want to use Trimmomatic to remove adapter sequences and low quality reads.
Under the IlluminaClip, there are following options:
TruSeq2 (SE, for Illumina GAII) TruSeq3 (SE, for MiSeq and HiSeq) TruSeq2 (PE, for Illumina GAII) TrueSeq3 (PE, for MiSeq and HiSeq) TruSeq3 (additional seqs) (PE for Miseq and HiSeq) Nextera (PE)
So far I have been using TruSeq3 (additional seqs), since it seemed like the most likely option - but I am not completely confident that it is right. I hope some experienced users maybe can help me out - I want to get it right and understand why I am choosing as I am.