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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 a small number of genomes. This interface is new in IGV 2.2; in previous versions the drop-down menu listed all available genomes hosted on the IGV server.

  • If you want to load a genome that is hosted on the server, but is not listed in the drop-down, select Genomes>Load Genome From Server.
  • To remove, reorder, and add genomes in bulk to the drop-down menu, select Genomes>Manage Genome List.

  • Reordering the list: Drag and drop genomes to reorder them in the list. 
  • Removing from the list: Select a genome and either press the Delete key or click the Remove button.
  • Adding to the list: Click Add from Server, which opens the following dialog.  Select the genomes you want to add to your genome list and click OK.

If the genome you need is not available, either post a request at http://groups.google.com/group/igv-help  that it be added, or follow the instructions below to load or import it.

Loading a Genome

This option supports defining a reference genome by loading either an IGV .genome file or a FASTA file.  The .genome file is created as described below. FASTA files must be plain text (not gzipped), and must be indexed with a .fai as defined by the Samtools suite (http://sourceforge.net/projects/samtools/). If the file is not indexed, IGV will attempt to index it.  IGV remembers the location of the FASTA file and the file will appear in the drop-down list until it is removed as described above (Genomes>Manage Genome List). 

Creating a .genome File

This option enables additional files to be associated with the FASTA reference sequence file, as described below. These files are archived in a zip with with a .genome extension. This option also allows the reference sequence to be defined as a directory of FASTA files, rather than a single FASTA.

Prerequisites:

  • Either (1) a FASTA file that contains the sequence data for each chromosome, or (2) a directory.  Directories of zip archives and gzipped FASTAs are no longer supported.
  • A cytoband file, which IGV uses to display the chromosome ideogram.  (Optional)
  • An annotation file, which IGV uses to display the reference gene track. The file can be in BED format, GFF format, or any variation of the genePred table format.  (Optional)
  • An alias file defining alternative names for chromosomes.  (Optional)

Note: If you are choosing files from the NCBI directory, you will generally want to use the .fna or .ffn file (nucleic acid sequences), as opposed to the .faa (amino acids). Choose the .gff file for the annotation file.

Step-by-step:

  1. Click Genomes>Create .genome File. IGV displays the a window where you enter the information.
  2. Enter an ID and a descriptive name for the genome.
  3. Enter the path on your file system or a web URL to the FASTA file for the genome.  If the FASTA file has not already been indexed, an index will be created during the import process. This will generate a file with a ".fai" extension which must be in the same directory as the FASTA file; thus it is necessary that the directory containing the file be writable. 
  4. Optionally, specify the cytoband file and the annotation (gene) file.
  5. If the sequence (chromosome) names differ between your FASTA and annotation files, you might need to create an alias file to provide a mapping between the different names. Certain well-known aliases are built into IGV and do not require an alias file. These include mappings that involve adding or removing the prefix "chr" to the name, for example  1 > chr1 and chr1 > 1.  Also, NCBI identifiers of the form  gi|125745044|ref|NC_002229.3| in a FASTA file will be mapped to names of the form NC_002229.3 in the corresponding GFF file. 
  6. Click Save. IGV displays the Genome Archive window.
  7. Select the directory in which to save the genome archive (*.genome) file and click Save. IGV saves the genome and loads it into IGV.

Removing an Imported Genome

To remove an imported genome:

  • Select Genomes>Manage Genome List. Select the genomes you want to remove and click Remove. Click Save to complete.