Fig. 2

Strategy for detecting and annotating repeats in galGal4. Our strategy comprised five successive steps: 1, definition of the number of repeats; 2, number of SSRs; 3, number of TEs; 4, definition of dark matter; 5, definition of CNVs. The final products of each of these 5 steps were stored in the bed or gff annotation files (yellow boxes). Arrows show the chronology of events in the processes in each step. Black ellipses show the various states of the genome analysed; blue boxes indicate the programs used; green boxes indicate the intermediate library produced by a given process; red boxes indicate the end of a process before editing the bed or gff annotation files. The purple box in step 5 indicates the source of the annotation file used for CNVs