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VariantSpark Notebook

AEHRC | 1.0.10

Linux/Unix, Ubuntu 18.04 - 64-bit Amazon Machine Image (AMI)

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    Lynn Langit

Try out VariantSpark in 15 minutes

  • November 27, 2019
  • Review verified by AWS Marketplace

The CSIRO Bioinformatics team has been creating a number of powerful bioinformatics tools for several years. This implementation of their VariantSpark tool, which allows for rapid discovery of polygenic disease associations in large whole-genome sequencing cohorts, lets you to quickly try out VariantSpark on AWS services and includes an example case from bioinformatics.

The example can be implemented via these AWS Marketplace CloudFormation templates and built in around 15 minutes. The example includes configuration for an EMR (Spark) cluster and parameters, VariantSpark parameters and a also a client EC2 machine which includes an example Jupyter notebook.

Running the example in the notebook takes less than 5 minutes. There you can see VariantSpark in action, finding significant variants in a fun, synthetic phenotype (Hipsterism - or the genetic traits linked to being a Hipster).

You can also visualize the impact of running the workload on the AWS EMR cluster, using the included Ganglia libraries. Ganglia is a scalable, distributed monitoring tool for high-performance computing systems, clusters and networks.

Because the solution is built on Cloud Formation templates, you can copy the solution template and further customize it quickly to support your production / research bioinformatics analyses.


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