Sold by: Orangenomix
Deployed on AWS
Orangenomix VEP annotates VCF files with variant consequences at scale, on AWS Batch, eliminating complex setup and reference data management. Let your team focus on the science, not infrastructure.
Overview
Orangenomix VEP: Cost-Effective Variant Effect Prediction on AWS
Orangenomix VEP delivers fast, scalable Variant Consequence annotations for your VCF files - without the complexity of managing reference data, storage, or compute infrastructure. Built on the trusted open-source Ensembl Variant Effect Predictor (VEP), Orangenomix VEP eliminates the barriers that make running VEP difficult and expensive.
The Challenge with Traditional VEP
Running the Ensembl Variant Effect Predictor on your own typically requires downloading and maintaining 20 to 30 GB of reference data. Teams must provision compute resources, manage storage, keep variant databases up to date, and troubleshoot configuration issues. This overhead slows down research timelines and drives up costs, especially when processing large-scale genomic datasets.
How Orangenomix VEP Solves This
Orangenomix VEP handles all of the setup, configuration, and infrastructure management so your team can focus on interpreting results rather than wrestling with tooling.
Key outcomes you can expect:
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Results in minutes, not hours - Feed your VCF files directly from Amazon S3 and start receiving Variant Consequence annotations quickly, with no manual provisioning required.
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Always up-to-date variant databases - Access the latest reference data automatically, without downloading or storing tens of gigabytes of files on your own infrastructure.
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Effortless scalability with AWS Batch - Process large genomic datasets at scale using AWS Batch, which dynamically provisions the compute resources you need and releases them when the job is done.
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No storage or compute management - Eliminate the operational burden of maintaining reference data storage and compute clusters. Orangenomix VEP takes care of provisioning and teardown.
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Cost-effective variant annotation - Run Variant Effect Prediction in the most cost-effective way on AWS, paying only for the resources your analysis actually consumes.
Seamless AWS Integration
Orangenomix VEP is designed to work natively with AWS services:
- Amazon S3 - Read input VCF files and write annotated results directly to your S3 buckets.
- AWS Batch - Automatically scale compute resources to match the size and complexity of your dataset.
This tight integration means there is no need to move data between platforms or configure complex pipelines. Your existing S3-based genomics workflows connect directly to Orangenomix VEP.
Who Is This For?
Orangenomix VEP is built for teams in healthcare and life sciences, bioinformatics, and data analytics who need reliable, scalable variant annotation:
- Genomics researchers analyzing whole-genome or whole-exome sequencing data
- Bioinformatics teams building or maintaining variant analysis pipelines
- Clinical genomics groups requiring consistent, up-to-date variant annotations
- Data science teams working with large-scale population genomics datasets
Get Started Quickly
With Orangenomix VEP, there is no complex installation or configuration process. Simply point the tool at your VCF files in Amazon S3, and the platform handles the rest - from provisioning compute through AWS Batch to delivering annotated results back to your S3 bucket. Start generating Variant Consequence annotations in minutes.
Highlights
- Zero Setup for Variant Effect Prediction: Orangenomix VEP eliminates the need to download and manage the 20 to 30 GB of reference data typically required by the open source Ensembl VEP tool. All reference databases are preconfigured and always kept up to date, so you can focus on your analysis rather than infrastructure. Simply point to your VCF files in Amazon S3 and start receiving annotated results in minutes.
- Scalable and Cost-Effective Genomic Analysis: Run variant consequence annotations efficiently over large datasets using AWS Batch. Orangenomix VEP handles compute provisioning automatically, delivering the most cost-effective way to run Variant Effect Prediction on AWS. There is no need to worry about storage capacity or scaling compute resources as your workloads grow.
- Seamless AWS Integration and Fast Results: Orangenomix VEP integrates directly with Amazon S3 for data input and output, enabling a streamlined workflow for genomics teams. Feed your VCF data from S3 and receive variant annotations quickly, with always-current variant databases ensuring your results reflect the latest available scientific knowledge.
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Pricing
Pricing is based on actual usage, with charges varying according to how much you consume. Subscriptions have no end date and may be canceled any time.
Additional AWS infrastructure costs may apply. Use the AWS Pricing Calculator to estimate your infrastructure costs.
Dimension | Description | Cost/unit |
|---|---|---|
vep_annotation_runs | Number of batches run | $0.00000002 |
Dimensions summary
You pay based on usage, measured by the number of annotation batches you run. There is one pricing dimension: vep_annotation_runs, charged per batch. Your cost scales directly with how many batches you process. Each batch runs on AWS Batch inside your own account, with data moving in and out of your S3 storage. If you run more batches, you pay for more units; if you run fewer, you pay less. There are no fixed tiers or instance-size choices to select.
Top-of-mind questions for buyers
A batch is one run of the annotation pipeline on AWS Batch. You drop VCF files into your S3 bucket and add a marker file to start a run. The pipeline creates one Batch job per sample. Results appear in a sibling S3 folder. Each triggered run counts toward your usage.
You are charged per batch you run, not per sample. When you drop more files, the compute fleet widens to match, then shuts down when done. Your batch count drives the software charge. Underlying AWS compute and S3 storage costs apply separately based on the resources your runs consume.
The vep_annotation_runs dimension charges per batch you actually run. If you deploy the CloudFormation stack but trigger no runs, no annotation charges accrue. You may still pay standard AWS fees for any resources the stack leaves running, but the software meter counts batches only.
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Deploy with Cloudformation
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- Amazon ECS
Container image
Containers are lightweight, portable execution environments that wrap server application software in a filesystem that includes everything it needs to run. Container applications run on supported container runtimes and orchestration services, such as Amazon Elastic Container Service (Amazon ECS) or Amazon Elastic Kubernetes Service (Amazon EKS). Both eliminate the need for you to install and operate your own container orchestration software by managing and scheduling containers on a scalable cluster of virtual machines.
Version release notes
This is an optimized version that delivers the best performance for Variant Annotation. This version delivers the most cost-effective way of running VEP on AWS.
Additional details
Usage instructions
Identify where your data lives on S3. Create and Drop your config file in the same folder. Drop a dummy '_READY' marker in the same folder. This will trigger processing in AWS Batch. Results end up in a folder named after input folder, but with the '_output' suffix. Monitor in Lambda. For more details check instructions.
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Vendor support
For support inquiries related to Orangenomix VEP, including usage questions, troubleshooting, and refund requests, please contact the Orangenomix team directly. Additional details on available support channels and response times will be provided upon subscription.
AWS infrastructure support
AWS Support is a one-on-one, fast-response support channel that is staffed 24x7x365 with experienced and technical support engineers. The service helps customers of all sizes and technical abilities to successfully utilize the products and features provided by Amazon Web Services.
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