View available reference genomes

Ion AmpliSeq™ Designer is pre-loaded with common public reference genomes for use in panel design for a variety of organisms, including human, mouse, chicken, cow, pig, sheep, dog, maize, rice, soybean, and tomato. You can also upload a custom reference. For more information on adding custom references, see Add a custom reference.

  1. In the navigation bar, click Genomes.

    The Design References screen opens, displaying pre-loaded public genomes.

    The list of public genomes in this screen is for informational purposes. You cannot select a public genome at this point. Click the links in the Assembly Version, Gene Annotation Sources, or Variant Sources columns in the row of a genome of interest to view the corresponding database information. Click the link the Reference Downloads column to download the reference FASTA file.

  2. To view previously uploaded custom references, click Custom References.

  1. Click to view previously-uploaded custom references.

  2. Click to view the assembly-specific reference information in UCSC Genome Browser.

  3. Click to navigate to the UCSC genome annotation database and download assembly-specific sequence and annotation data for a reference.

  4. Click to navigate to available variant source catalogues for a reference.

  5. Click to download the nucleotide sequence for a reference in FASTA file format.

  6. Click to add a new custom reference. For more information, see Add a custom reference.

Related Topics
Parent topic: Get started with Ion AmpliSeq™ Designer