A method for large scale scaffolding of a genome assembly comprising: generating (i) a chromosome interaction dataset from a set of reads from a genome of interest produced by a chromosome conformation analysis technique, and (ii) a test set of contigs from aligning the set of reads with a draft assembly sequence, a reference assembly sequence, or both; subjecting the chromosome interaction dataset and the test set of contigs to a computer-implemented method, the method comprising: clustering the test set of contigs to form two or more location cluster groups by building a graph using the chromosome interaction dataset and performing a hierarchical agglomerative clustering algorithm, each location cluster group comprising one or more location-clustered contigs, wherein the two or more location cluster groups are two or more chromosome groups, each chromosome group comprising one or more contigs derived from the same chromosome; ordering each of the one or more location-clustered contigs within each of the two or more location cluster groups to form an ordered set of one or more location-clustered contigs within each cluster group by building a graph using the chromosome interaction dataset and calculating a minimum spanning tree; and orienting each ordered set of one or more location-clustered contigs to assign a relative orientation to each of the location-clustered contigs within each location cluster group by building a graph and calculating an orientation quality score for each location-clustered contig using the chromosome interaction dataset. generating (i) a chromosome interaction dataset from a set of reads from a genome of interest produced by a chromosome conformation analysis technique, and (ii) a test set of contigs from aligning the set of reads with a draft assembly sequence, a reference assembly sequence, or both; subjecting the chromosome interaction dataset and the test set of contigs to a computer-implemented method, the method comprising: clustering the test set of contigs to form two or more location cluster groups by building a graph using the chromosome interaction dataset and performing a hierarchical agglomerative clustering algorithm, each location cluster group comprising one or more location-clustered contigs, wherein the two or more location cluster groups are two or more chromosome groups, each chromosome group comprising one or more contigs derived from the same chromosome; ordering each of the one or more location-clustered contigs within each of the two or more location cluster groups to form an ordered set of one or more location-clustered contigs within each cluster group by building a graph using the chromosome interaction dataset and calculating a minimum spanning tree; and orienting each ordered set of one or more location-clustered contigs to assign a relative orientation to each of the location-clustered contigs within each location cluster group by building a graph and calculating an orientation quality score for each location-clustered contig using the chromosome interaction dataset. clustering the test set of contigs to form two or more location cluster groups by building a graph using the chromosome interaction dataset and performing a hierarchical agglomerative clustering algorithm, each location cluster group comprising one or more location-clustered contigs, wherein the two or more location cluster groups are two or more chromosome groups, each chromosome group comprising one or more contigs derived from the same chromosome; ordering each of the one or more location-clustered contigs within each of the two or more location cluster groups to form an ordered set of one or more location-clustered contigs within each cluster group by building a graph using the chromosome interaction dataset and calculating a minimum spanning tree; and orienting each ordered set of one or more location-clustered contigs to assign a relative orientation to each of the location-clustered contigs within each location cluster group by building a graph and calculating an orientation quality score for each location-clustered contig using the chromosome interaction dataset.