The invention provides methods of manufacturing alkanes from triglyceride oils produced through fermentation of oil-bearing microbes. The processes provided herein can utilize a variety of carbohydrate feedstocks including cane bagasse, sugar beet pulp, corn stover, glycerol, corn starch, sorghum, molasses, waste glycerol, and other renewable materials. These processes further comprise hydrotreating, hydrocracking, isomerization, distillation, and other petrochemical processes for use with oil-bearing microbes and products derived therefrom to manufacture fuels. Particular embodiments include the manufacture of ASTM D975 and ASTM D1655 compliant fuels. Genetically engineered microbes provided herein can be used in the manufacture of renewable diesel and renewable jet fuel.