Scripts: https://github.com/johnsolk/ONT_Illumina_genome_assembly Raw ONT and Illumina reads: https://www.ebi.ac.uk/ena/data/view/PRJEB29136 [](https://doi.org/10.5281/zenodo.3251034) Johnson, Lisa K., Brown, C. Titus, & Whitehead, Andrew. (2019). Draft genome assemblies of killifish from the Fundulus genus with ONT and Illumina sequencing platforms [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3251034 ABSTRACT Draft de novo reference genome assemblies were obtained from four North American killifish species (Fundulus xenicus, Fundulus catenatus, Fundulus nottii, and Fundulus olivaceus) using sequence reads from Illumina and Oxford Nanopore Technologies’ PromethION platforms. For each species, the PromethION platform was used to generate 30-45x sequence coverage, and the Illumina platform was used to generate 50-160x sequence coverage. Contig N50 values ranged from 0.4 Mb to 2.7 Mb, and BUSCO scores were consistently above 90% complete using the Eukaryota database. Draft assemblies and raw sequencing data are available for public use. We encourage use and re-use of these data for assembly benchmarking and external analyses.