I used trimmomatics to trim my Illumina Hiseq reads with a list that I downloaded from here.
But after I assembled the trimmed reads, I tried to upload the assembly to the TSA database in NCBI, they gave me the error saying that my sequence is contaminated by primer sequences. I found one of the contamination sources using vector screen, which is
CCCTACACGACGCTCTTCCGATCT. But this sequence is actually contained in one of the adapter sequences in the list:
So my question is why the sequence is not trimmed off by trimmomatics?
Is there anyway to remove the contamination from the assembly. So I don't have to go back to reassemble the sequences?