Stable pipeline and ROI_finder postprocessing scripts

Stable pipeline release with functional ROI_finder postprocessing scripts including readme.

First functional

This first functional release of the pipeline:

1. takes a set of queries and references sequences in fasta format
2. performs sequence alignments using the nucmer program (MUMMER4)
3. filters the alignments based on their length, identity percentage and N content.
4. It finally calculates the alignment percentage for each query-reference combination and creates a final result matrix from these alignments.
5. Additionally, the delta files of the alignments are also output due to their potential value in post-processing.