During the act of genome sequence alignment, we are not able to sequence the entire genome. Normally, the result is a number of smaller sequences which we call contigs. Contigs are partially assembled smaller pieces which yet need to be assembled into an entire genome (a set of chromosomes). One of the methods used for this process uses data about chromatin interactions between contigs, specifically, the method used here uses Hi-C data [8]. The Hi-C data needs to be aligned along the contigs and we need to measure the number of links between chromosomes, between contigs and inside the contigs themselves. These links, along with the very distribution of chromatin, follows a set distribution with the help of which we can draw conclusions. The produced data is analyzed and, using the knowledge we gathered about the links, the contigs are first separated into specific chromosomes, then ordered within the chromosomes and lastly, oriented into the right direction. The first step is based on the fact that the contigs have more mutual links within the chromosomes they belong to. The second step follows the idea that neighboring contigs have more mutual links that those contigs that are further apart, and this linkage density falls linearly with contig distance. The third and last step comes from the knowledge that neighboring contig ends (tails) have more links that contig ends that are further apart. During the whole process, it is vital to take note of the fact that chromatin density is not equally distributed among all contigs and some will have a statistically higher likelihood of having an interaction with other contigs simply from the fact that they have more dense (frequent) Hi-C links. Finally, the output data is assembled into chromosomes and we compare the results with reference data. The program has been tested on fruit fly (Drosophila melanogaster) datasets and human (Homo sapiens) datasets. This thesis is based on a paper [2].