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Loading and Managing Genomes in IGV 2.2

In previous releases, the genome drop-down menu listed all genomes available in IGV. However, the list of hosted genomes has grown beyond the point where it is managable in a single drop-down menu. In IGV 2.2 you can customize the drop-down to include only the genomes that are of interest to you. The genome menu now will initially list only a small number of default genomes, but you can add genomes to the list, remove genomes from the list, and rearrange the order of genomes in the list. 

Selecting a Reference Genome

As before, you typically select a reference genome by clicking on it in the genomes drop-down menu. If you want to use a genome that is hosted by IGV, but is not listed in the menu, select Genomes>Load Genome From Server. This will open a dialog with a scrollable list of all available genomes. You can narrow down the list by entering a partial name in the Filter field. Select the genome you want and click OK. It will be added to the drop-down menu, and also loaded and displayed in the IGV window.

You can also load a reference genome from a FASTA file or an IGV .genome file by selecting Genomes>Load from File or Genomes>Load from URL. The new genome will be added to the drop-down menu, and also loaded and displayed in the IGV window. 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. See below for details on how to create an IGV .genome file. 

Managing the Genomes Menu

To remove genomes from the drop-down menu, add genomes to the menu in bulk, or change the order of the genomes in the menu, select Genomes>Manage Genome List. This will open a dialog with a list of all the genomes in the drop-down menu.

  • To remove an entry from the drop-down menu, select the genome from this list and either press the Delete key or click the Remove button.
  • To add multiple genomes to the drop-down menu, click on Add From Server to open a dialog with a scrollable list of all available genomes, similar to above. Select one or more genomes from the list and click OK. Note that this will not change the reference genome being displayed in the IGV window; it only adds genomes to the drop-down menu.
  • Rearrange the entries in the menu by selecting items on the list and dragging them to the desired location. 

Once you have made all your changes to the list in the Manage Genome List dialog, click Save. Or click Cancel to back out the changes.

Creating a .genome File

This option allows you to associate additional files with the FASTA reference sequence file, as described below. These files are archived in a zip with with a .genome extension. This option also supports defining the reference sequence 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. This will create the .genome file, add the genome to the genomes drop-down menu, and load it as the reference genome displayed in the IGV window.