So I have pacbio and MinION reads and I want to know if a genetically modified region is 1 time present or multiple times. Normal mapping doesn't give me the answers that I want as the reads are soft-clipped on the known sequence so I have no information about what else is in the read. So instead of using the known sequence as reference and the reads as query I was thinking about using the reads in a multi-fasta file as a reference and use the known sequence as query. Which tool is the best for this? a local BLAST? Or am I thinking in a wrong way.