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Downloading Hosted Genomes for Offline Use
This page describes how to download a genome specification (json) file and configure it for use in IGV without an internet connection. This requires downloading all dependent files, including the sequence. The following example uses C. elegans (ce11); for other genomes see the Hosted Genomes list below.
NOTE: Some of the more frequently used genomes are available for download here as a package ready for offline use. If you download one of these packages, skip to step 4 below.
For our ce11 example: curl -O https://s3.amazonaws.com/igv.org.genomes/ce11/ce11.json
{
"id": "ce11",
"name": "C. elegans (ce11)",
"fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa",
"indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa.fai",
"cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/ce11/cytoBandIdeo.txt.gz",
"tracks": [
{
"name": "Refseq Genes",
"format": "refgene",
"url": "https://s3.amazonaws.com/igv.org.genomes/ce11/refGene.sorted.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/ce11/refGene.sorted.txt.gz.tbi",
"indexed": false,
"order": 1000000,
"removable": false,
"visibilityWindow": -1
},
{
"name": "Genes",
"format": "bed",
"url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_ce11.bed.gz",
"hidden" : true,
"searchable": true
}
]
}
For our example, these files are:
- https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa
- https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa.fai
- https://s3.amazonaws.com/igv.org.genomes/ce11/cytoBandIdeo.txt.gz
- https://s3.amazonaws.com/igv.org.genomes/ce11/refGene.sorted.txt.gz
- https://s3.amazonaws.com/igv.org.genomes/ce11/refGene.sorted.txt.gz.tbi
- https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_ce11.bed.gz
Your local copy of the .json file should reference the downloaded files. Reference can be by URL to a file on your local network, or by file path, which can be relative to the location of the .json file. Assuming the downloaded data files are in the same directory as the .json file, the ce11.json file will look like this:
{
"id": "ce11",
"name": "C. elegans (ce11)",
"fastaURL": "ce11.fa",
"indexURL": "ce11.fa.fai",
"cytobandURL": "cytoBandIdeo.txt.gz",
"tracks": [
{
"name": "Refseq Genes",
"format": "refgene",
"url": "refGene.sorted.txt.gz",
"indexURL": "refGene.sorted.txt.gz.tbi",
"indexed": false,
"order": 1000000,
"removable": false,
"visibilityWindow": -1
},
{
"name": "Genes",
"format": "bed",
"url": "geneLocations_ce11.bed.gz",
"hidden" : true,
"searchable": true
}
]
}
Load the updated .json genome specification file into IGV using the Genomes > Load from File... menu.
NOTE: If you previously loaded the same genome into IGV using the regular hosted options, you may need to delete its json file to prevent conflicts with the local version. The hosted-based files can be found in the folder <userhome>/igv/genomes.
List of specification files for IGV hosted genomes as of March 29, 2022.
[Note: Not all IGV genomes have a corresponding .json file that can be downloaded for local use.]