Hi, apologies for this basic questions, I new in NGS quality control. I have been check my NGS data (Illumina - HiSeq 2500 2*100pb) using FastQC after trimming Nextera Adaptater with bbduck (BBTool package) using trimming overlap (ktrim=r k=25 mink=11 hdist=1 tpe tbo). And the checks fails Per base sequence content, Per sequence GC content and Kmer Content. My question is should I be trying remove the first base (~15) of my sequence? When I try this, Kmer Content fails again but at the end of the sequence. Should I remove again at the end?
After my goal is to assemble them with a De Bruijn assembler and thus i'm afraid of over-represent kmer. 


Thanks for the help.

![enter image description here][1]
![enter image description here][2]


  [1]: https://i.imgsafe.org/498873a.png
  [2]: https://i.imgsafe.org/8d597c0.png
In fragmentation the Nextera kit enzyme prefers to cut DNA from certain places, which is probably the reason for the bias you observe. I would let it be..