Q: What does the Genomics Secondary Analysis Using AWS Step Functions and AWS Batch solution do?

A: The solution creates a scalable environment in AWS to develop, build, deploy, and run genomics secondary analysis pipelines. You can build and deploy updates to both the genomics workflows, and the infrastructure that supports their execution.

Q: Can I modify the solution to run my own genomics analysis?

A: Yes, you can modify the solution to fit your particular needs, for example, by adding new containerized tools and creating new workflows. Each change will be tracked by the CI/CD pipeline, facilitating change control management, rollbacks, and auditing.

Q: What bioinformatics tools are supported?

A: This solution supports containerized bioinformatics tools. This includes tools that you build yourself from source or pre-existing container images from public or private container image repositories. To get you started quickly, this solution builds the following open source bioinformatics tools as container images: BWA–Burrows-Wheeler Genomic sequence aligner, SAMtools–utilities for analyzing and manipulating genomics alignments, and BCFtools–utilities for variant calling and manipulating VCFs and BCFs.

Q: What bioinformatics workflow is used in the solution?

A: This solution includes an AWS Step Functions state machine that implements a simple genomics variant calling workflow using BWA-MEM, SAMtools, and BCFtools. The workflow aligns raw FASTQ files to a reference sequence, and call variants on a specified list of chromosomes using dynamic parallelism.

Q: Can I deploy the solution in any AWS Region?

A: No, this solution uses the AWS CodePipeline service which is currently available in specific AWS Regions only. Therefore, you must launch this solution in an AWS Region where this service is available.. For the most current availability by region, see AWS service offerings by region.

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