Input Reference (Sequence, Genome, for Scaffolding, etc.)

If any version of the Reference Sequence screen appears, you must input some type of reference sequence or genome template package before proceeding further in the wizard. The screen has different names depending on the workflow you are following. Some names include: Input Reference Sequence for Scaffolding, Input Reference Sequence, Input Reference Genome, Input Draft Genome or Contigs, Input High Quality Draft Genome, and Input Reference Sequence for Scaffolding. Versions of the screen vary slightly from one another.

*Note: If you are setting up a gene homology alignment in MegAlign Pro, click here for information on the specialized version of this screen used in that workflow.

Optional pre-import steps for the Reference Sequence screen:

• Annotate reference sequences prior to import
• Manually specify an isoform prior to import
• Make a custom VCF file
• Make a custom BED file
• Troubleshoot a Manifest file

Add and remove reference sequence files or draft genomes:

SeqMan NGen can read and produce output using a variety of common chromosome naming conventions, including “chr1” and “ch1,” as well as Arabic and Roman numerals. See our Supported File Types page for allowable file extensions.

• Add a reference sequence or draft genome from your computer or the Cloud
• Add a genome template from DNASTAR – (RECOMMENDED) Genome template packages include dbSNP information that is very useful for downstream analysis.
• Add a genome template from NCBI
• Use RNA-Seq de novo transcriptome output as a reference
• Remove a sequence from the list

Options pertaining only to the Reference Sequence screen:

• Specify a VCF, BED or Manifest file

Click Next > to proceed to the next wizard screen or < Back to return to the previous screen.