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Hosting Genomes

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Jim Robinson edited this page Jul 14, 2020 · 8 revisions

Instructions for hosting reference genomes on your own server.

There are many ways to create the required files, this is just one. In this example we'll host a single genome, human hg38.

  • Download the IGV genome list from https://s3.amazonaws.com/igv.org.genomes/genomes.txt

  • Open the downloaded genomes.txt file in a plain text editor and eliminate all lines except the first and the genome(s) of interest. For this example the file contents should be as shown below. Note the format is 3-column tab delimited: descriptive name, url to .genome file, and ID. The ID is arbitrary but for UCSC hosted genomes please use their ID. This is important for the blat tool, which uses the UCSC blat server.

<Server-Side Genome List>
Human hg38	https://s3.amazonaws.com/igv.org.genomes/hg38/hg38.genome	hg38

  • Download the ".genome" file from the URL (second field in genomes.txt). In this example https://s3.amazonaws.com/igv.org.genomes/hg38/hg38.genome.

  • Move the .genome file to an empty working directory. This is important for the next steps

  • The .genome file is a zip archive, unzip it. The exact command might vary by platform.

unzip hg38.genome
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