Sequencing eukaryotic genomes is more difficult than sequencing genomes of bacteria or archaea because of the

Are there options? because there are lots of answers. 

Firstly, eukaryotic DNA tends to be much longer; it's held inside a nucleus, so it has to be separated from the rest of the cell; and there are also mitochondria in most eukaryotic cells, which have their own RNA, which has to be separated.