AWS HealthOmics service is designed to help healthcare and life sciences organization to store, process, and analyze large-scale omics data such as Genomics, Transcriptomics, and Proteomics.
It provides a fully managed solution for handling complex bioinformatics workflows, enabling users to run analysis workflows with high performance and scalability.
AWS HealthOmics provides robust infrastructure that allows for efficient data processing and reduces the need for on-premises resources, offering cost-effective and secure data management.
In this blog post, we share how scientists with little to no experience in Bioinformatics, Computational Workflows and AWS can use Quark to perform omics data analysis using AWS HealthOmics.
Quark Overview
Quark’s mission is to help scientists extract actionable insights from omics data faster, with greater accuracy and with end to end reproducibility.
With its intuitive, scientist-friendly user interface, the platform allows users to easily run and manage Multi-omics, Computational Biology and AI/ML Workflows without the need for advanced technical expertise.
By leveraging AWS Cloud infrastructure, the platform efficiently processes large datasets, offering both scalability and faster analysis times. This ensures that users can handle the data with greater flexibility and efficiency in their workflows and analytics.
Quark also supports building customizable workflows, results visualization, multi-omics data analysis, and integrates seamlessly with AWS HealthOmics.
This makes it an ideal solution for advancing drug development, personalized medicine and research in the field of life sciences.
Quark’s Key Capabilities
Scientist friendly experience: Quark provides the most simplified and intuitive experience for Bench Scientists and Bioinformaticians to run large scale, reproducible workflows and get actionable insights.
Seamless Workflow Submission: Users can submit Workflows effortlessly without any programming/technical expertise or navigating complex procedures. Quark out-of-the-box provides various Workflows from nf-core, AWS HealthOmics and third-party commercial providers.
AI-powered Analytics: Effortlessly compare cohorts, perform differential expression, enrichment analyses, conduct pathway and disease association studies. By uncovering meaningful patterns and correlations within your data, Quark’s AI-driven analytics accelerate the discovery process while offering you insights that directly impact your research outcomes.
Simplified Data & Metadata Management: Users can easily upload omics data or bring data from third-party data sources (SFTP, S3, etc.) and seamlessly analyze them through the platform. Metadata can be easily managed to ensure easy discoverability of data and standardization across an organization.
Easily Build New Pipelines: Build new pipelines by using a Visual Drag and Drop interface without any programming expertise. You do not need to know Nextflow, CWL or WDL. Simply use Quark’s Visual Pipeline Builder, connect the tools and build an end-to-end pipeline in a matter of minutes.
Quark + AWS HealthOmics
Quark makes it super simple to run AWS HealthOmics Workflows and generate insights from omics data.
- User’s can discover all the AWS HealthOmics Ready2Run Workflows from a central catalog and run them in 1-click. Quark orchestrates the Workflow execution in AWS HealthOmics.
- Manage the input data required for AWS HealthOmics Workflows through the data management feature offered by Quark. Quark manages the underlying storage and users do not have to deal with S3 or AWS HealthOmics storage directly.
- Directly download results of the Workflow execution or analyze them through integrated visualization tools.
- Get detailed timeline of the Workflow execution to understand resource utilization and execution times of various tasks and access to logs to troubleshoot any issues with the Workflow execution.
- Create cohorts between different patient or sample groups, compare different cohorts and perform interactive analysis such as Gene Enrichment, Differential Expression, Pathway and disease association studies.
Quark + AWS HealthOmics in action
All AWS HealthOmics Ready2Run Workflows available centrally in a catalog called “Launchpad”.
Select any Workflow that you like to run and navigate to the input form to provide the required inputs.
Provide the required inputs by selecting the files that you have already organized through Quark’s Data Management feature called “My Files”.
Note: You can also upload input files at this step by clicking on the “Action” dropdown.
Review the input details and start the Workflow run.
Monitor the progress of your AWS HealthOmics Workflow executions from the “Runs” tab.
Get detailed execution summary, timeline. Troubleshoot any issues by accessing the logs.
Download the results generated from the AWS HealthOmics Workflow execution.
Powerful Analytics for AWS HealthOmics Workflows
Quark provides out of the box rich and powerful Analytics for AWS HealthOmics Workflows.
You can create cohorts between different groups and compare them effortlessly through our out-of-the-box dashboards.
Search any samples that were processed by providing the Gene or Variant information.
Get a list of matching Samples and Variants. Filter sample tables based on the available metadata such as patient ID, sex or status which is a tumour or normal status of the sample.
Save them as a Cohort. You can create many such cohorts based on your study requirements.
Select two cohorts for comparison and click on the “Compare” button.
Quark performs Gene Enrichment Analysis and produces interactive visualizations so that you can analyze the cohort further.
Final Thoughts
Using Quark, you can run AWS HealthOmics Workflows seamlessly through the simplified user experience that we have built for scientists.
In 1-click, you can run large scale, reproducible omics workflows and get instant access to powerful Analytics to generate insights.
Quark runs within your AWS account and has been designed with all the necessary AWS security best practices such as Encryption, Fine Grained IAM, Role Based Access Controls.
By choosing a platform such as Quark, you can focus your efforts on new scientific discoveries and faster, personalized patient care while Quark takes care of all the heavy lifting related to computational workflows, data management and analytics for omics data.
If you are interested to learn more about Quark, schedule a demo here.