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| 00-Genomics-Basics | ||
| 01-Data-Migration | ||
| 02-Cromwell-Azure | ||
| 03-Nextflow-Azure | ||
| 05-Data | ||
| 96-Resources | ||
| 98-Appendix | ||
| 99-Images | ||
| CODE_OF_CONDUCT.md | ||
| LICENSE | ||
| README.md | ||
| SECURITY.md | ||
| SUPPORT.md | ||
README.md
Project
The field of Genomics is intimidating for a lot of people. The vocabulary and terminology makes it hard to get started. Given the massive computational needs of the genomics field today, we need more technical people learning about genomics and helping practitioners build scalable and secure systems. Our goal is to make this topic more approachable.
Our target is anyone who is working in technology today that wants to help their company, customer or just the favorite project build better solutions. Our focus is on the Azure cloud, but with some adjustments, the same patterns could be used elsewhere.
If you are new, follow the guide sequentially. If you are looking for a specific product or service, feel free to jump to that section.
Genomics Basics
In this section we review the biological terms and concepts that you should be familiar with. We define DNA, RNA, Chromosomes, Genes and introduce the central dogma. If you are new to the study of genetics or need a refresher, start here.
Pipeline Basics
In this section we introduce genomic pipelines. Why they are necessary and the key steps involved. We cover reference genomes, alignment and variant calling and some basic analysis.
We'll also introduce some of the common workflow engines out there, mostly focusing on Cromwell and Nextflow.
Data Migration.
Genomics datasets tend to be very large. If you have accumulated a lot of data on-premises and are looking for best practices around moving the data to the cloud, this section has a couple of options
Cromwell on Azure
Use this guide to get started on Cromwell on Azure.
Nextflow on Azure
Azure has native support for Nextflow. Use this guide to get started on Nextflow on Azure.
Feedback
We opened this project for collaborating and contributions from anyone making this journey. If you would like to contribute, please check the guidelines below.
Contributing
This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.
When you submit a pull request, a CLA bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA.
This project has adopted the Microsoft Open Source Code of Conduct. For more information see the Code of Conduct FAQ or contact opencode@microsoft.com with any additional questions or comments.
Trademarks
This project may contain trademarks or logos for projects, products, or services. Authorized use of Microsoft trademarks or logos is subject to and must follow Microsoft's Trademark & Brand Guidelines. Use of Microsoft trademarks or logos in modified versions of this project must not cause confusion or imply Microsoft sponsorship. Any use of third-party trademarks or logos are subject to those third-party's policies.