Many Bioinformatics workflows require aligning things to genomes, or some kind of genome 'context' in which to operate. iMaps therefore provides reference genomes for common model organisms, which can be easily selected when running these pipelines. The files for a genome are generated by the Prepare Genome pipeline.
Each species will have one 'reference genome' - the public, iMaps-provided default version for that species - and there may be others that can be used as well. Anyone can run the Prepare Genome pipeline to generate versions of those genomes that are best suited to your research if the defaults do not suffice.