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Loading a Genome

IGV displays annotations for one genome at a time. To load a different genome, select it from the genome drop-down list in the tool bar:

  • When you switch genomes, all data that is currently loaded in the browser is cleared, starting a new session (as if you had selected File>New Session).
  • The genome selected when IGV exits is automatically selected when IGV restarts.

Selecting a Hosted Genome

IGV provides a number of genomes that are hosted on a server at the Broad Institute. Initially, the genome drop-down lists only these hosted genomes. If the genome you need is not available, either contact igv-help(at)broadinstitute.org and request that it be added or import the genome.

Importing a Genome

If the genome drop-down list does not include the genome that you need, you can easily import it. Imported genomes appear at the top of the genome drop-down list, above the hosted genomes.

Prerequisites:

  • A FASTA file, directory of FASTA files, or zip of FASTA files that contains the sequence data for each chromosome in the genome.  (Required)
  • A cytoband file, which IGV uses to display the chromosome ideogram.  (Optional)
  • An annotation file in  BED file format, the GFF file format, or any variation of the genePred table format.  (Optional)

Note: If you are choosing files from the NCBI directory, you will almost always want to use the .FNA file for the FASTA, and the .GFF file for the annotation file.
 

Step-by-step:

  1. Click File>Import Genome. IGV displays the Import Genome window:
  2. Enter an ID and name for the genome.
  3. For Fasta File, click the ellipse button and select the FASTA file (or zip or directory of FASTA files) that contains the sequence data. NOTE: If your FASTA files are a directory, you MUST select the Fasta file is a directory checkbox.
  4. Optionally, specify the cytoband file and the gene track annotation (Gene File) file.
  5. If the sequence (chromosome) names differ between your fasta and annotation files you might need to create  an alias file to map between the two.  An exception is NCBI genomes that sequence names  in the fasta file
  6. with the form  gi|125745044|ref|NC_002229.3|, but use names of the form NC_002229.3 in the corresponding gff file.  IGV will attempt to map these names automatically.   If you do not see any annotations after loading your imported genome, it is likely due to sequence name mismatch.
  7. You can also specify a sequence URL for a web-hosted genome.  This is a URL to the base directory for the "<seqname>.txt" files created during the import step.
  8. Click Save. IGV displays the Genome Archive window.
  9. Select the directory in which to save the genome archive (*.genome) file and click Save. IGV saves the genome and loads it into IGV.

When genomes are imported from a single FASTA file, the order of the sequences in the FASTA file is preserved in the Chromosome drop-down list.

Removing an Imported Genome

To remove an imported genome:

  • Click File>Remove Imported Genomes.