The red raspberry, Rubus idaeus, is a major commercial fruit valued for its taste and high antioxidant content. Genomic resources are needed to improve research and breeding of this high value crop. Using a hybrid approach of both long and short sequence reads, a de novo genome was assembled consisting of 2,145 scaffolds with a genome completeness of 95.3% and an N50 score of 638 KB. 35,566 protein coding genes were annotated with a transcriptome completeness score of 97.2%. This resource contributes to phylogenetic and comparative studies of the agriculturally valuable Rosaceae family. Comparing the raspberry and strawberry transcriptomes reveal numerous transcription factors, both shared and unique, with roles in meristem regulation. Further, a comparative electronic fluorescent pictograph (eFP) web viewer was constructed to enable visualization of RNA expression patterns of orthologs across Rosaceae species.