HIGH QUALITY INDIVIDUAL ANIMAL GENOME ASSEMBLIES WILL HELP IN REACHING ONE OF THE CENTRAL GOALS OF GENETIC STUDIES: DETERMINING THE RELATIONSHIP BETWEEN PHENOTYPE AND GENOTYPE. DISCOVERING GENETIC FEATURES GOVERNING GROWTH, MEAT QUALITY, FEED EFFICIENCY AND DISEASE RESISTANCE ARE OF THE UTMOST IMPORTANCE FOR LIVESTOCK BREEDING PROGRAMS. IDEALLY ONE WOULD LIKE TO BE ABLE TO DETERMINE THE COMPLETE GENOMIC SEQUENCE OF MANY DIFFERENT INDIVIDUALS AND THEN PERFORM STUDIES BASED THE SNP DATA AND ON DISCOVERING STRUCTURAL VARIATION BY ALIGNING THEIR GENOME SEQUENCES TO EACH OTHER. BUT PRESENTLY THIS IS COST-PROHIBITIVE, CONFOUNDED BOTH BY THE SEQUENCING COSTS TO PRODUCE LONG READ DATA FOR HIGH QUALITY DE NOVO ASSEMBLY OF A MAMMALIAN GENOME AND BY HIGH COMPUTATIONAL COSTS. THE LONG-TERM GOAL OF THIS PROJECT IS TO ADDRESS THESE ISSUES BY DEVELOPING COMPUTATIONAL TECHNIQUES THAT USE INEXPENSIVE ILLUMINA DATA AND ALLOW FOR FAST COMPUTATION ON INEXPENSIVE HARDWARE, AND THAT YIELD HIGH QUALITY ASSEMBLIES OF INDIVIDUAL GENOMES AIDED BY SYNTENY TO ONE OR MORE REFERENCE GENOMES FOR THE SAME OR CLOSELY RELATED SPECIES.