The genome of the Swanson doubled haploid (DH) YY male line of rainbow trout was de novo assembled using the Canu pipeline, high-coverage PacBio long-read sequence data, Bionano optical maps, and Hi-C proximity ligation sequence data, resulting in 29 major scaffolds aligning with the karyotype of the Swanson line (2 N = 58). This assembly, totaling 2.3 Gb with an N50 of 52.4 Mb, represents approximately 95% of the genome in 29 chromosome sequences with only 109 gaps between scaffolds. Notably, corrections to previous errors in the Swanson line genome assembly were made, including the identification of a double large inversion on the Omy05 chromosome (~57 Mb), the absence of the Omy20 inversion between the Arlee and Swanson assemblies, and the discovery of a ~6.7 Mb inversion on Omy26. This comprehensive assembly contributes to refining the rainbow trout reference genome and serves as a valuable resource for future genetic studies within this species.