AWS HPC Blog
Author: Olivia Choudhury
Olivia Choudhury, PhD, is a Senior Partner Solutions Architect at AWS. She helps partners, in the Healthcare and Life Sciences domain, design, develop, and scale state-of-the-art solutions leveraging AWS. She has a background in genomics, healthcare analytics, federated learning, and privacy-preserving machine learning. Outside of work, she plays board games, paints landscapes, and collects manga.
Intel Open Omics Acceleration Framework on AWS: fast, cost-efficient, and seamless
With genomics and multi-omics research generating more data than ever, the Open Omics Acceleration Framework from Intel Labs aims to provide a highly productive platform for researchers. Check out recent results in this new blog post.
Running accurate, comprehensive, and efficient genomics workflows on AWS using Illumina DRAGEN v4.0
In this blog, we provide a walkthrough of running Illumina DRAGEN v4.0 genomic analysis pipelines on AWS, showing accuracy and efficiency, copy number analysis, structural variants, SMN callers, repeat expansion detection, and pharmacogenomics insights for complex genes. We also highlight some benchmarking results for runtime, cost, and concordance from the Illumina DRAGEN DNA sequencing pipeline.
Cost-effective and accurate genomics analysis with Sentieon on AWS
In this blog post, we benchmark the performance of Sentieon’s DNAseq and DNAscope pipelines using publicly available genomics datasets on AWS. You will gain an understanding of the runtime, cost, and accuracy performance of these germline variant calling pipelines across a wide range of Amazon EC2 instances.
Accelerating Genomics Pipelines Using Intel’s Open Omics Acceleration Framework on AWS
In this blog, we showcase the first version of Open Omics and benchmark three applications that are used in processing NGS data – sequence alignment tools BWA-MEM, minimap2, and single cell ATAC-Seq on Xeon-based Amazon Elastic Compute Cloud (Amazon EC2) Instances.
Getting Started with NVIDIA Clara Parabricks on AWS Batch using AWS CloudFormation
In this blog post, we’ll show how you can run NVIDIA Parabricks on AWS Batch leveraging AWS CloudFormation templates. Parabricks is a GPU-accelerated tool for secondary genomic analysis. It reduces the runtime of variant calling on a 30x human genome from 30 hours to just 30 minutes, and leverages AWS Batch to provide an interface that scales compute jobs across multiple instances in the cloud.