To find PAV sequences present in in assembly_1 (presence-assembly) but absent in assembly_2 (absence-assembly), the pipeline performs the following steps:
1. The presence assembly assembly_1 contigs/scaffolds are shred in chunks of 1000 bases after removal of Ns
2. The 1000 bases chunks are mapped against the absence assembly assembly_2
3. groups of consequent 1000 bases chunks that are not find in the absence assembly assembly_2 are merged and printed out as 'absence PAVs'