Amazon Genomics CLI Overview.

What is the Amazon Genomics CLI?

Amazon Genomics CLI is an open source tool for genomics and life science customers that simplifies and automates the deployment of cloud infrastructure, providing you with an easy-to-use command line interface to quickly setup and run genomics workflows on Amazon Web Services (AWS) specified by languages like CWL, Nextflow, Snakemake, and WDL. By removing the heavy lifting from setting up and running genomics workflows in the cloud, software developers and researchers can automatically provision, configure and scale cloud resources to enable faster and more cost-effective population-level genetics studies, drug discovery cycles, and more.

Why do I want it?

Amazon Genomics CLI is targeted at bioinformaticians and genomics analysts who are not experts in cloud infrastructure and best practices. If you want to take advantage of cloud computing to run your workflows at scale, but you don’t want to become an expert in high performance batch computing and distributed systems then Amazon Genomics CLI is probably for you.

  • What is it good for?: Abstracting the infrastructure needed to run workflows from the running of the workflows by hiding all the complexity behind a familiar CLI interface. When you need to get your workflows running quickly and are happy to let the tool make the decisions about the best infrastructure according to AWS best practices.

  • What is it not good for?: Situations where you want, or need, complete and fine-grained control over how your workflows are run in the cloud. Where specifying exactly how they run, and what infrastructure is used, is just as important as running them.

  • What is it not yet good for?: Let us know, we’d love to hear your suggestions on how we can make the tool work for you.

Where should I go next?

Take a look at the following pages to help you start running your workflows quickly: