I sequenced BAC DNA using Oxford Nanopore MinION. These are large ranging from 1000 to 200,000 basepairs long raw sequences. I want to remove the vector sequence attached to the BAC sequence. The vector sequence is ~7500 base pairs long. I used stand alone BLAST and I got only 64 BLAST hits, this is unexpected. I have a total of 272849 BAC raw sequences (from nanopore) in my input file. So, I can't believe the BLAST result. I want to trim vector sequence before I assemble. I appreciate if anybody could help me with this.