To load the reference files
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 reference genome. Note the following about the required reference:
• For all application types other than transcriptome, STR analysis, or Mitochondrial amplicon analysis:
• If you are aligning the data against a small genome (one that is less than or equal to 250 Mbp), then you can align data against a reference file that is in either .fasta format or GenBank format. See To load a GenBank or .fasta reference file (Reference < 250 Mbp).
 | You can download GenBank format references from the NCBI website (http://www.ncbi.nlm.nih.gov/). For information about NextGENe’s alignment algorithms, see NextGENe Sequence Alignment Algorithms. |
• 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. See To load a preloaded reference.
• If you are detecting structural variations, then you must align the data against a preloaded reference that contains both DNA and RNA sequences, either Human_v37.p13+mRNA or Human_v38.p12+mRNA.
| | For detailed instructions about importing preloaded references, see the NextGENe and Mutation Surveyor Reference and Track Manager Tool User’s Manual. For detailed information about building a custom preloaded reference, see the Geneticist Assistant User’s Manual or Online Help. For detailed information about the algorithm that NextGENe uses to align reads to a preloaded reference, see NextGENe Sequence Alignment Algorithms. |
• The transcriptome application type always requires a preloaded reference that is created from an annotated GenBank file or supplied by SoftGenetics. See Transcriptome Alignment Project with Alternative Splicing in the NextGENe Sequence Alignment Tool.
• The STR application type requires a custom .fasta reference file. See STR Analysis Project in the NextGENe Sequence Alignment Tool.
• The Mitochondrial amplicon application type requires the mitochondrial Genbank reference file. You must also load a BED file that details the amplicon locations. See To set ROI regions from a BED or GBK file.