Supporting data for "Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish"

Whole genome sequencing data from wild-caught individuals of closely-related North American killifish species (<i>Fundulus xenicus</i>, <i>Fundulus catenatus</i>, <i>Fundulus nottii</i>, and <i>Fundulus olivaceus</i>) were obtained using long-read Oxford Nanopore Technology (ONT) PromethION and short-read Illumina platforms. <br>Draft <i>de novo</i> reference genome assemblies were generated using a combination of long and short sequencing reads. 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. Illumina-only assemblies were fragmented with high numbers of contigs while ONT-only assemblies were error prone with low BUSCO scores. The highest N50 values, ranging from 0.4 Mb to 2.7 Mb, were from assemblies generated using a combination of short and long read data. BUSCO scores were consistently above 90% complete using the Eukaryota database. <br>Good quality genomes can be obtained from a combination of using short read Illumina data to polish assemblies generated with long read ONT data. Draft assemblies and raw sequencing data are available for public use. We encourage use and re-use of these data for assembly benchmarking and other analyses.