Raw DNA-seq reads from Amoebophrya sp. ex Karlodinium veneficum (NCBI BioProject PRJNA257290; SRA accession: SRX730949) were quality and adapter trimmed using BBDuk v36.92 (part of BBTools) and assembled onto contigs and scaffolds using SPAdes v3.15.4 (Bankevich et al. 2012, J Comput Biol) in default settings.