Drosophila melanogaster (D.mel) is a commonly used model system organism that is widely used in research. From D.mel various cells from different tissues and developmental stages has been isolated and immortalized to produce whats termed a "cell line". One D.mel cell line is the Schneider S2 (S2) cell line. It is known that the genome of S2 cells are heavily rearranged compared to the D.mel fly, yet no reference genome exist for the S2 cell (and to many other cell lines). Still, a lot of research is done on cell lines but use the reference genome of the living organism when performing analysis of genomic data.
Given the above, we wish to study what genomic rearrangements and to which extent have occurred in S2 cells compared to the D.mel fly. Furthermore, we will investigate the context of such rearrangements. Our goal is to finally produce a reference genome for the S2 cell.