The NextGENe Sequence Alignment tool matches short sequence reads to a reference sequence. For all application types other than de novo Assembly, a reference is required for aligning the reads of the data file that is being analyzed against a known genome. If you are aligning the data against a small genome (one that is less than or equal to 250 Mbp), then you must align data against a reference that is either in .fasta format or GenBank (gbk or gb) 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 must 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.