Single red spherule cell and sperm were isolated from the same S.purpuratus sea urchin using limiting dilution followed by visualization of sperm by live/dead staining with Hoechst and propidium iodide. All single cells were processed directly for whole genome amplification (WGA) by the multiple displacement amplification method. Genomes were sequenced by MinION Nanopore. Few sequencing runs were combined and reads were cleaned from adapter sequences by Porechop.