Rapid development and commercialization of instruments that can accurately, rapidly, and cheaply sequence billions of DNA bases is revolutionizing molecular biology and medicine. Because a reference genome is usually available, the first bioinformatics challenge presented by the new generation of high-throughput sequencers is the genome mapping problem, where each read is mapped to a reference genome to reveal its location(s). An introduction to mapping algorithms, as well as factors that influence their results, is provided here.