The major histocompatibility complex class I (MHC-I) genes are highly polymorphic. MHC-I genotyping is required for determining the peptide epitopes available to an individual’s T-cell repertoire. Current genotyping software tools do not work for the dog, due to very limited known canine alleles. To address this, we developed a Kmer-based paired-end read (KPR) de novo assembler and genotyper, which assemble paired-end RNA-seq reads from MHC-I regions into contigs, and then genotype each contig and estimate its expression level. KPR tools outperform other popular software examined in typing new alleles. We used KPR tools to successfully genotype152 dogs from a published dataset. The study discovers 33 putative new alleles, finds dominant alleles in 4 dog breeds, and builds allele diversity and expression landscapes among the 152 dogs. Our software meets a significant need in biomedical research. Display omitted •KPR software genotypes DLA-I alleles and estimates expression using RNA-seq data•KPR performs de novo assembly and outperforms other tools in typing new alleles•Typing 152 dogs uncovers 33 putative new alleles and dominant alleles in 4 breeds•DLA-12 and DLA-88L alleles cluster with DLA-88 alleles Biocomputational method; Computational bioinformatics; Genomic analysis