Dramatic improvements in DNA sequencing technologies have led to a more than 1,000-fold reduction in sequencing costs over the past five years. Genome-wide research approaches can thus now be applied beyond medically relevant questions to examine the molecular-genetic basis of behavior, development and unique life histories in almost any organism. A first step for an emerging model organism is usually establishing a reference genome sequence. I offer insight gained from the fire ant genome project. First, I detail how the project came to be and how sequencing, assembly and annotation strategies were chosen. Subsequently, I describe some of the issues linked to working with data from recently sequenced genomes. Finally, I discuss an approach undertaken in a follow-up project based on the fire ant genome sequence.