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Genomes on the Cloud (GotCloud)

To handle the increasing volume of next generation sequencing and genotyping data, we created and developed software pipelines called Genomes on the Cloud (GotCloud) for:

  • Mapping
  • Variant Calling

Key Features:

  • Scalable to tens of thousands of samples
  • Robust against unexpected system failure using GNU make
  • Massively parallel, can run hundreds of jobs
  • Easy to use - Automates series of configurable steps
  • Available on Amazon Web Services (AWS) Elastic Compute Cloud (EC2)
  • Run on local machines/clusters
  • Available via Debian Packages

The following describes the use of this software with the Amazon Web Services (, but you can just as easily use the pipelines on your own machine(s) by just installing them.

Join in GotCloud mailing list

Please join in the GotCloud Google Group to ask / discuss / comment about these pipelines.

AWS Specific Setup

Preparation in AWS

Resources / Cost

Development Notes

General Usage

Install the Software (for AWS or a local machine)

Run the Software