Tag: Genomics

Check out this post to learn how linter rules for Nextflow’s DSL can help you catch errors in your workflows before runtime, which means greater developer productivity, which leads directly to a faster time to science.

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.

In this second part of using Nextflow for machine learning for life science workloads, we provide a step-by-step guide, explaining how you can easily deploy a Seqera environment on AWS to run ML and other pipelines.

Nextflow is popular workflow framework for genomics pipelines, but did you know you can also use it for machine-learning? ML is already being used for medical imaging, protein folding, drug discovery, and gene editing. In this post, we explain how to build an example Nextflow pipeline that performs ML model-training and inference for image analysis.

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.

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.

Calling budding bioinformaticians! If you learn through hands-on practicals and walkthroughs, AWS and GIS have developed training and resources to help you increase the scale and productivity of your research using the AWS cloud.

Today we are excited to announce that all 9000+ applications provided by the BioContainers community are available within ECR Public Gallery! You don’t need an AWS account to access these images, but having one allows many more pulls to the internet, and unmetered usage within AWS. If you perform any sort of bioinformatics analysis on AWS, you should check it out!

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.

In this blog post, we demonstrate how to leverage the AWS Genomics Command line and Amazon SageMaker to analyze large-scale exome sequences and derive meaningful insights. We use the bioinformatics workflow manager Nextflow, it’s open source library of pipelines, NF-Core, and AWS Batch.