The article is about sequencing technology. This is what is needed to get from physical DNA to its textual representation. The assignment to chromosomes is lost in the process. It can either be reconstructed after sequencing, by e.g. whole genome assembly or k-mer based methods.

But there are other methods of identifying races than looking at correctly identified SNPs. Often, k-mer content is enough. And it is likely more efficient, because it does not require any computationally heavy assembly.