Evaluation of Oxford Nanopore Technology Minion for genome sequencing of aquatic pathogens. Folder contains a curated, complete reference-quality genome of Streptococcus iniae, an important bacterial pathogen of tilapia and other warm water fish species, assembled from PacBio and Illumina HiSeq data. The same strain (QMA0248) was sequenced using ONT Minion and an assembly prepared from subsampled reads to provide ~100 fold coverage. For comparison, alignment of the two assemblies was performed in progressive mauve single nucleotides polymorphisms (SNPs) called. A total of 5685 SNPs were detected in the 2.1MB genome, representing a basecall error rate of only 0.284%. A tab-delimited text file of the SNPs and positions in the ref genome are included in the folder. These SNPs will be mapped onto epidemiologically relevant genes that MLST-type and cps serotype.