Loading a Genome

Genomes are selected from the genome drop-down list on the upper-left of the IGV window.  Intially, this list contains a single item, Human hg18 or Human hg19, depending on the version of IGV.  To add other genomes to the list, see the sections below on "Selecting a Hosted Genome" and "Loading Other Genomes".

  • 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.  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 or click on the More... entry at the bottom of the drop-down list. This will bring up a list of all the genomes on the server. The genomes are listed in alphabetical order. Scroll down to find the one you want, or use the 'Filter' to search.

  • Select the genome you would like to add to the IGV genomes menu, and click 'OK'. A new entry will be inserted in the drop-down list (in alphabetical order), and the display will switch to this genome.
  • Checking the 'Download sequence' box will also download a FASTA file of the whole genome sequence for offline use. All available genomes are listed, even those that have already been loaded into the IGV drop-down menu. This is in case you want to now download the sequence for a genome already in the menu. Note that a downloadable FASTA file is not available for all hosted genomes. A notice will pop up if you try to download a sequence that is not available.

Loading Other Genomes

If you have the .FASTA file for your reference genome sequence, it can be loaded by clicking on Genomes > Load Genome from File or Genomes > Load Genome from URL. In this case, the gene annotations will not be loaded automatically, but if you have the gene annotation file, it can be loaded like any other data file via the Files > Load from menus. An alternative is to package all the genome information into a single .genome file, as described below. 

FASTA files must can be plain text or block gzipped, and must be indexed with a .fai as defined by the Samtools suite (http://sourceforge.net/projects/samtools/). If the file is plain text (not block gzipped) and 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  (Advanced)

In special cases it might be desirable to create a .genome file to define the reference.  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 not 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 a Genome

To remove a genome from the IGV menu:

  • Select Genomes>Remove Genomes.
  • Select the genomes you want to remove and click Remove. Click Save to complete.
  • Note that you cannot remove the currently selected genome.