AWS iGenomes

Common reference genomes hosted on AWS S3

This resource hosts commonly used bioinformatics reference genomes with the help of a grant from AWS Programs for Research and Education.

In order to get the references, you need to sync the files from S3 to your EC2 environment. This web page contains two tools to help you with that - a command builder and a command-line script.

For more information about this resource, please see the GitHub readme at

Sync command builder

Use the dropdown boxes below to build an AWS S3 sync command for your reference.

Currently just eu-west-1
Available variables: {genome}, {source}, {build}, {type_path}
Bucket URL
waiting for selection…
Sync command
waiting for selection…
Loading file manifest..

Command-line Script

You can use a bash script we've written which can be used to easily obtain reference genomes where you need them. This builds the required command using either command-line prompts or flags, then runs the sync command for you.

Note that you need to have the aws command line tools installed and set up with proper authentication.

Quick usage

Paste this command in your terminal to download and run the script directly.

curl -fsSL | bash
Advanced usage

You can save the script locally and run it with command-line flags as follows:

curl -fsSL >
bash --help

 		[-g <genome name>]
 		[-s <source name>]
 		[-b <build name>]
 		[-t <reference type>]
 		[-o <output directory>]
 		[-d (dry run, no downloads)]
 		[-q (quiet mode, non-interactive)]
 		[-h (usage help)]

All command line flags are optional. If not specified
and not running in quiet-mode, the script will prompt
for input and show available options.

Please note that this script requires the AWS command
line tools to be installed and configured for authenticated

Script source:

Script URL:

If you have any questions or feature requests, please create an issue.