Typically, if you are aligning your data files against a small genome (one that is less than or equal to 250 Mbp), then you align data against a reference file that is either in .fasta format or GenBank format. If you are aligning the data against a large genome (one that is greater than 250 Mbp, such as the whole human genome), then you align the data against a preloaded reference that SoftGenetics supplies or a custom preloaded reference that was built using the NextGENe Build Preloaded Reference tool. For special data application types, however, such as ChIP-Seq or small RNA analysis, after you align your files to a reference genome, you might then need to align your data files against a reference sequence that you create using NextGENe’s Peak Identification tool.