# DRAGEN on AWS

You can run DRAGEN analysis on Amazon Web Services (AWS). For information on using DRAGEN, see the [DRAGEN User Guide Section](https://help.dragen.illumina.com/product-guides/dragen-v4.5). For information on using AWS, see the AMI documentation available on the Amazon Web Services site.

## Getting Access to the DRAGEN AMI (Amazon Machine Image)

There are two options available for using the AMI: a Marketplace AMI (Pay-As-You-Go) and a Private AMI (Bring-Your-Own-License). To use the Marketplace AMI, visit the AWS Marketplace and subscribe to the DRAGEN Complete Suite. For access to the Private AMI, please contact our [sales team](https://www.illumina.com/company/contact-us.html) to obtain licensing and deployment instructions. Also, please refer to the [Cloud Licensing Reference Section](https://help.dragen.illumina.com/reference/licensing/cloud_licensing) for more information.

## Launch an Instance

To launch an EC2 instance, refer to the [AWS EC2 Launch Guide documentation](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/LaunchingAndUsingInstances.html) - making sure you select the desired DRAGEN AMI and instance type.

* For instance type, an [EC2 FPGA-powered instance](https://aws.amazon.com/ec2/instance-types/f2/) is required. f2.6xlarge instance type is recommended for DRAGEN if regionally available, otherwise f1.4xlarge.
* For configure storage, we recommend attaching 2TB of EBS storage using 4x 500GB GP3 volumes configured as RAID0, if local instance storage is insufficient

## Connect to and Configure Your Instance

1. Navigate to the Instances page and select the instance to connect to.
2. Click **Connect**, then choose **SSH client**.
3. instanceUse appropriate username: ec2-user for EL8 images, or centos for EL7 images.
4. Mount the disks to `/staging` on the instance using the following commands as needed.

```
sudo yum -y install mdadm
sudo mdadm --create --verbose /dev/md0 --level=0 --name=MY_RAID0 --raid-devices=<number of volumes> <device name 1> <device name 2>
sudo mkfs.ext4 -L MY_RAID0 /dev/md0
sudo mkdir -p /staging
sudo sh -c "echo 'LABEL=MY_RAID0 /staging ext4 defaults,noatime 0 0' >> /etc/fstab"
sudo mount -a
```

For example, the following command mounts four volumes attached at `/dev/nvme1n1`, `/dev/nvme2n1`, `/dev/nvme3n1`, and `/dev/nvme4n1` to a RAID 0 on `/staging`.

```
sudo yum -y install mdadm
sudo mdadm --create --verbose /dev/md0 --level=0 --name=MY_RAID0 --raid-devices=4 /dev/nvme1n1 /dev/nvme2n1 /dev/nvme3n1 /dev/nvme4n1
sudo mkfs.ext4 -L MY_RAID0 /dev/md0
sudo mkdir -p /staging
sudo sh -c "echo 'LABEL=MY_RAID0 /staging ext4 defaults,noatime 0 0' >> /etc/fstab"
sudo mount -a
```

## Data Flow

Input files, including the [hash table](https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/product_files.html), must be downloaded to the instance. DRAGEN can also process large input files (e.g., FASTQ, BAM) directly from s3 or a pre-signed URL. Ensure the instance has access to the s3 bucket via local credentials or an IAM role.

## Simple Run Example

```
cd /ephemeral/
wget https://webdata.illumina.com/downloads/software/dragen/resource-files/hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1.tar.gz
mkdir /ephemeral/hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1
tar xvfz hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1.tar.gz -C hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1
wget https://ilmn-dragen-giab-samples.s3.amazonaws.com/WES/HG002/NA24385-AJ-Son-R1-NS_S33_L001_R2_001.fastq.gz 
wget https://ilmn-dragen-giab-samples.s3.amazonaws.com/WES/HG002/NA24385-AJ-Son-R1-NS_S33_L001_R1_001.fastq.gz

dragen \
-r /ephemeral/hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1 \
--fastq-file1 /ephemeral/NA24385-AJ-Son-R1-NS_S33_L001_R2_001.fastq.gz \
--fastq-file2  /ephemeral/NA24385-AJ-Son-R1-NS_S33_L001_R2_001.fastq.gz \
--RGID NA24385_RGID \
--RGSM NA24385 \
--enable-map-align true \
--enable-map-align-output true \
--enable-duplicate-marking true \
--enable-variant-caller true \
--intermediate-results-dir /ephemeral/ \
--output-file-prefix NA24385 \
--output-directory /ephemeral/ 
--lic-server <LICENSE> # needed for private AMI users
```

You can use DRAGEN command-line options. For more information on DRAGEN analysis and command line options, see the [Command Line Options Section](https://help.dragen.illumina.com/product-guides/dragen-v4.5/command-line-options) of the user guide. For information on using AWS, see the AMI documentation available on the Amazon Web Services site.

Note: As stated in the [Cloud Licensing Reference Section](https://help.dragen.illumina.com/reference/licensing/cloud_licensing), if running DRAGEN in a container with IDMSv2 - make sure to increase your hop count to at least 2.


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