Fig. 2

Schematic overview of ARPEGGIO’s structure. All the shapes follow the flowchart standardized symbols [47]. Ovals show the beginning and ends of the workflow. Diamonds represent conditional rules in ARPEGGIO’s configuration file and those rules make ARPEGGIO more adaptable to the needs of the user. Each conditional rule can be set to “true” (tick) or “false” (cross). Besides the first conditional rule, all other rules stop the workflow at the given point when set to “false”. The different grey backgrounds and the white background represent different Conda environments used by ARPEGGIO to carry out different steps of the analyses. In the scheme, the background of each step represents the environment that the step is part of. The bottom of each background shows the name of the file used to create the environment. At the top all the tools used by ARPEGGIO are shown and vertically aligned their corresponding step in the workflow. From the alignment and deduplication step, ARPEGGIO executes two workflows in parallel for each progenitor side, both highlighted by the dashed areas