The extended Scipio workflow. This diagram depicts the activity and data flow of a Scipio run. Scipio needs a protein and a target genome sequence, both in FASTA format, as input to start a Blat run. Every single Blat hit is subsequently processed and filtered, and assembled in the case of hits on multiple targets. The gap_length describes the number of amino acids of an unmatched query subsequence. The intron_length is the corresponding length of the unmatched target subsequence in nucleotides.