We have been assembling the genomes of many Drosophila species. With that in mind, we developed this protocol to keep the cost of sequencing down to <$500 per assembly while maintaining a decent number of very long reads. Using these guidelines, a typical Drosophila Nanopore sequencing run should have read N50 of 20-40kbp with 5-15% of data in reads >100kbp. Sequencing is halted at about 40-50X depth of coverage (8-10 Gbp for most species). This of course depends on the quality of the sample, quality and quantity of the prepared library, and the frequency at which the flow cell is flushed and reloaded. We typically run 3-4 species per 2 flow cells, usually for ~14-18 Gbp of data per flow cell. This protocol borrows several elements from John Tyson's "Rocky Mountain" protocol and we thank him for several insightful discussions. https://www.protocols.io/view/rocky-mountain-adventures-in-genomic-dna-sample-pr-7euhjew